normalize: Normalize a metabolomics dataset
In crmn: CCMN and Other Normalization Methods for Metabolomics Data
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Normalization methods for metabolomics data
Usage
1
Arguments
object
an ExpressionSet
method
the desired method
segments
normalization in a cross-validation setup, only to use for
validation/QC purposes.
...
passed on to normFit and normPred
Details
Wrapper function for normFit and normPred
Value
the normalized dataset
Author(s)
Henning Redestig
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
data(mix)
normalize(mix, "crmn", factor="type", ncomp=3)
#other methods
normalize(mix, "one")
normalize(mix, "avg")
normalize(mix, "nomis")
normalize(mix, "t1")
normalize(mix, "ri")
normalize(mix, "median")
normalize(mix, "totL2")
## can also do normalization with matrices
Y <- exprs(mix)
G <- with(pData(mix), model.matrix(~-1+type))
isIS <- with(fData(mix), tag == "IS")
normalize(Y, "crmn", factor=G, ncomp=3, standards=isIS)
Example output
Loading required package: pcaMethods
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘pcaMethods’
The following object is masked from ‘package:stats’:
loadings
Attaching package: ‘crmn’
The following object is masked from ‘package:BiocGenerics’:
normalize
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
STDs_1_2_1 STDs_1_2_2 STDs_1_2_3 STDs_1_3_1 STDs_1_3_2
15 42270693455 79813641464 62138560028 9.549550e+10 76956860360
18 1585976779 236918025 15768318093 1.116093e+10 73224501
47 3526793897 6135787546 4612524807 6.562883e+09 4099527809
51 28727285644 67217864436 44862206527 6.924001e+10 45671361861
52 4427597052 6763648607 5439439497 7.813281e+09 5396280421
56 7441691693 16566166368 10200900497 1.975485e+10 8779389559
58 140457728991 252393006147 173267295323 2.797450e+11 193302340239
59 5805487741 20699981668 8485729106 2.541731e+10 8851689536
61 16074447890 13914467888 11103652798 3.805633e+10 32510538205
72 8269615301 18023371096 9810547209 1.913980e+10 10568495046
76 50920341113 75365008959 54224254427 1.201478e+11 78695858855
83 1238038243 2846684989 1549350187 3.070157e+09 1483192392
88 55788988494 90945126632 55973565381 2.016199e+11 148544557540
91 27732966164 86302027892 34940201178 1.009936e+11 37364482053
96 63202595094 87685522620 99165764209 1.041214e+11 45429864674
99 37285155920 83401440694 45794828935 1.168215e+11 50066020875
100 25359841232 70113413225 22385741553 1.040998e+11 42863275353
101 6267398512 29118203394 12993724464 4.073640e+10 8992758261
104 2390335230 15206635497 3937922974 2.086045e+10 4409278084
108 5551637784 10289231741 5050698802 1.399565e+10 5548696252
110 15467394112 20289432548 16017717035 2.835453e+10 13933559364
114 402402513497 667212999322 433710121382 1.145646e+12 438282862583
117 44235363372 60432776558 36339400913 1.303982e+11 63146254189
121 2350846248 2383121627 1848696689 1.834055e+10 1870734025
124 3465334679 6248822882 3878625721 2.860431e+10 7861423352
125 701317456 801751534 380424083 1.500798e+09 1005196964
126 246202662 592787893 279904898 1.085224e+09 248966223
127 91563022237 122333359163 93487387514 2.424798e+11 80631388016
160 1723814957 3258106689 1715185887 7.097407e+09 2638375170
161 949809418 5228203453 1074765504 1.628670e+10 1736445177
213 39130162 128332965 82901657 2.495666e+08 58733636
215 489950720 942143485 842280831 1.036102e+09 577197578
217 15158366384 85010379317 33253559529 1.066290e+11 24705763766
223 117026248 468261788 203050408 7.359517e+08 161616949
249 107813980 96171889 58875955 2.440207e+08 180093177
STDs_1_3_3 STDs_2_1_1 STDs_2_1_2 STDs_2_1_3 STDs_2_2_1
15 75010783749 9.555348e+09 7.134046e+09 6.853384e+09 7.034869e+09
18 21681359180 2.761876e+10 1.950810e+10 8.948037e+10 2.933949e+10
47 5423063600 2.520831e+10 1.851556e+10 2.349083e+10 1.922214e+10
51 57656993568 2.071207e+11 1.422851e+11 1.996128e+11 1.517924e+11
52 6135985161 3.990635e+10 4.005675e+10 3.868305e+10 3.634357e+10
56 13523567647 9.082425e+10 7.328525e+10 8.179510e+10 6.958371e+10
58 211755827412 2.100347e+10 1.534581e+10 1.446463e+10 1.534828e+10
59 13950873794 4.940696e+10 4.053220e+10 4.742963e+10 3.404221e+10
61 12327451421 3.332152e+09 2.112612e+09 1.741369e+09 2.263492e+09
72 13543347065 1.803916e+11 1.450110e+11 1.971707e+11 1.419434e+11
76 63414736898 2.338107e+11 1.585346e+11 2.338519e+11 1.759188e+11
83 2102283783 1.802098e+10 1.644348e+10 1.988222e+10 1.425008e+10
88 81074143552 7.254881e+11 4.950776e+11 6.609316e+11 4.937580e+11
91 54214119701 7.161547e+09 4.704187e+09 3.912173e+09 4.760500e+09
96 39612521217 1.208625e+10 7.691634e+09 6.816257e+09 8.716165e+09
99 63214107525 2.377051e+11 1.559830e+11 1.958846e+11 1.652958e+11
100 33752487630 1.180161e+10 7.370869e+09 4.952936e+09 8.376151e+09
101 22886317954 5.968560e+10 3.822043e+10 5.578889e+10 3.591506e+10
104 8382669159 1.693421e+09 1.223522e+09 1.276877e+09 1.047175e+09
108 7135998235 6.766793e+10 4.517514e+10 5.533502e+10 5.093137e+10
110 19553088628 1.190313e+11 8.067676e+10 1.086343e+11 9.799135e+10
114 635139161914 1.632465e+12 1.001129e+12 1.587189e+12 1.194458e+12
117 43774621877 2.142720e+11 1.370798e+11 1.709833e+11 1.846162e+11
121 2154380628 4.572226e+08 7.679945e+07 9.602150e+07 1.790931e+08
124 6087442089 7.665869e+10 3.826853e+10 6.992107e+10 5.083174e+10
125 423602799 1.296620e+09 4.383309e+08 6.796225e+07 1.087719e+09
126 457232955 4.867662e+09 2.312149e+09 3.250615e+09 3.207918e+09
127 116218226910 7.775563e+09 4.373757e+09 5.547087e+09 7.822436e+09
160 2695383526 1.125607e+09 3.787050e+08 5.062768e+08 9.726216e+08
161 2735460570 2.873677e+10 1.137963e+10 2.321683e+10 1.503062e+10
213 151719923 1.484724e+09 1.049124e+09 1.357375e+09 9.210870e+08
215 1106069945 5.454540e+09 5.141207e+09 6.311006e+09 4.581682e+09
217 66859570482 5.003973e+09 3.812508e+09 5.663840e+09 2.963841e+09
223 367729514 1.735860e+09 1.045057e+09 1.661789e+09 1.062922e+09
249 82096366 2.457915e+07 1.664941e+07 1.933582e+07 2.461825e+07
STDs_2_2_2 STDs_2_2_3 STDs_2_3_1 STDs_2_3_2 STDs_2_3_3
15 1.004828e+10 6.241870e+09 1.010163e+10 9.831291e+09 8.403516e+09
18 4.137106e+09 7.773814e+10 5.576874e+10 7.877096e+09 1.410028e+11
47 2.806378e+10 2.062458e+10 2.470496e+10 2.671047e+10 2.733098e+10
51 2.322868e+11 1.792538e+11 2.051970e+11 2.221660e+11 2.320415e+11
52 4.526602e+10 3.739765e+10 4.204741e+10 4.611995e+10 4.668027e+10
56 1.074974e+11 7.361460e+10 9.652446e+10 1.062041e+11 1.031245e+11
58 2.275979e+10 1.309482e+10 2.110163e+10 2.165548e+10 1.827739e+10
59 6.518585e+10 4.124044e+10 5.881808e+10 6.832425e+10 6.317563e+10
61 3.067962e+09 1.572813e+09 3.550440e+09 2.905126e+09 1.789692e+09
72 2.090836e+11 1.869965e+11 1.906256e+11 1.988704e+11 2.486657e+11
76 2.383028e+11 2.118971e+11 2.420150e+11 2.252833e+11 2.661898e+11
83 2.187930e+10 1.852608e+10 1.988835e+10 2.169279e+10 2.502001e+10
88 8.343073e+11 6.016269e+11 8.204417e+11 8.036685e+11 7.493921e+11
91 7.875875e+09 3.304762e+09 8.102287e+09 7.293070e+09 5.926175e+09
96 1.037039e+10 9.318858e+09 1.104407e+10 4.244209e+09 1.157301e+10
99 2.528343e+11 1.749558e+11 2.567638e+11 2.422465e+11 2.365353e+11
100 1.230937e+10 4.397820e+09 1.376289e+10 1.169404e+10 6.082376e+09
101 7.755080e+10 4.800951e+10 7.279799e+10 7.516272e+10 7.657146e+10
104 2.612365e+09 1.111437e+09 2.336324e+09 2.428709e+09 1.826664e+09
108 6.664684e+10 4.927776e+10 7.277440e+10 6.197013e+10 6.418220e+10
110 1.072021e+11 1.019515e+11 1.218898e+11 9.830618e+10 1.243989e+11
114 1.582232e+12 1.441088e+12 1.749609e+12 1.513251e+12 1.704714e+12
117 1.908377e+11 1.610008e+11 2.487462e+11 1.752054e+11 1.949258e+11
121 1.302160e+08 1.731239e+08 3.157305e+08 1.469368e+08 5.970648e+07
124 7.048831e+10 5.741248e+10 1.056301e+11 7.504254e+10 9.402054e+10
125 7.679793e+08 3.897844e+07 1.365416e+09 7.088795e+08 1.287430e+08
126 3.898400e+09 2.569002e+09 5.911560e+09 3.720173e+09 4.155117e+09
127 6.721401e+09 5.002176e+09 9.775062e+09 5.566900e+09 5.665427e+09
160 5.770342e+08 1.730097e+08 1.630580e+09 5.924180e+08 6.386275e+08
161 2.943782e+10 1.687650e+10 3.708756e+10 2.862992e+10 3.410166e+10
213 1.687643e+09 1.089441e+09 1.765339e+09 1.895280e+09 1.918399e+09
215 6.367717e+09 6.030505e+09 5.957383e+09 6.787141e+09 7.412499e+09
217 7.011393e+09 4.871120e+09 6.353766e+09 7.488186e+09 8.688316e+09
223 1.883053e+09 1.233549e+09 2.324103e+09 1.829068e+09 2.054823e+09
249 2.264114e+07 1.704520e+07 2.924462e+07 2.068004e+07 1.490853e+07
STDs_3_1_1 STDs_3_1_2 STDs_3_1_3 STDs_3_2_1 STDs_3_2_2
15 32129302305 69629740623 58510814230 35711882800 73819842388
18 33096458970 50997159141 301622847945 33639050108 50238064145
47 1712669075 2930969833 1814221054 1873341261 2928058313
51 5929716543 11598048699 7017055274 6394483611 12700014233
52 47209386445 76336154688 65717466511 48962520675 80407473837
56 129523642350 302973504134 223892840431 139091044535 314216389909
58 96760635409 186061334931 141651087869 103292791306 192402571847
59 2045276218 7751395656 4241261796 2295214784 8216346472
61 7710348409 12957731987 6283148863 7261319971 14509013418
72 266609635932 546970727979 497879066310 283847989820 552132244814
76 10358738158 15660722408 11190247857 10973108482 15577397750
83 22851423276 52743156363 46947495110 24603428024 54714247996
88 19763671299 46659584609 27915224737 21705932854 54861363270
91 22482914712 67545252776 43500643322 24444722993 74502180270
96 36449892521 46905043748 32075906566 38934878209 47267864522
99 12602199654 28130032621 19547351553 14021083262 29423116745
100 16126681399 47840386404 30619527539 17564191202 51302602003
101 1822513349 9484150025 4423348010 2236706681 9099639207
104 3754169789 25718536702 12584261918 4408325951 24767982450
108 97773325287 176352564650 144604480263 105875352191 181763710039
110 200147882325 262204979628 263149725218 208928170440 264367466829
114 120757101551 198564124041 138203711636 133718216818 206140969476
117 6336406351 8883066504 5325643001 6544936971 9200050518
121 1284927850 2227923023 500641901 972028316 994019599
124 529029210 771687411 897999355 474893442 902318318
125 1045898597 945009869 432752054 1132216979 1001561124
126 6350083101 13442399497 13359369669 7250404489 14282851587
127 37325385374 50384884807 46041803903 41560342985 34681537100
160 1279684574 2219432896 1393337412 1365738115 2445925732
161 782677912 5311331743 2530055042 924022667 6532515157
213 1694417817 7361730179 5207003124 1922042917 8517724633
215 7067311580 14401715220 14184376790 7498269069 15029566028
217 12134343059 77327854079 54515133266 13983791410 83880522741
223 2382871412 7360424984 8612411951 2713624608 8403600946
249 47210237 43703857 34856492 48290249 47436771
STDs_3_2_3 STDs_3_3_1 STDs_3_3_2 STDs_3_3_3 STDs1_1_1
15 64417603554 35510859891 62131428503 58819970598 112507642440
18 201410244088 25921151660 39458222895 192335643569 6898383871
47 2088809374 1839922659 2617343958 2061344247 3830288544
51 7636731941 6633910914 11364750713 6570088204 70400029787
52 59123740044 47507007667 66568444106 56191917913 5576899002
56 222492074712 134101237145 240412107271 191744239883 12912248564
58 160405864930 101486445365 165360986695 138425098586 267941894524
59 4194380924 2291844562 5365817379 3217037241 12328431439
61 6711329901 7011295204 12785890231 5988188477 30936857243
72 515472733230 271787257341 460580285264 438160627049 27230148140
76 11969120235 10518400230 13570236516 10460792072 102162409624
83 42356300421 24204892290 41480892348 36140501879 1882892883
88 29765133738 21379425997 40421694160 23627097043 185195802466
91 44513363860 23698765659 50225173756 32470049055 50908356303
96 48668321631 19146612138 43881789918 49926557990 87767490106
99 22016080837 13503821135 22692571437 17950156049 77804551670
100 32163775216 16678864127 36145529889 23925678384 51575451535
101 5093928789 1913077177 6243586520 3476066219 11033121629
104 12937421578 4164355821 14708997735 7345562309 5065021939
108 132692591465 103024512441 142819816186 111283741940 7421050806
110 252988704437 200327089965 231448930494 226038579119 17988656469
114 145152249542 128824397953 168155288670 121836028676 739281202177
117 5207976701 6162991230 8053998551 3997279349 97945029117
121 1704958496 1441243166 585663575 700726818 9866325871
124 773409670 471633420 665623851 555857068 11947631874
125 463729069 1031149833 1036802853 383229027 620047630
126 11535543907 6927943873 8612073459 8588256555 495192441
127 47780402428 31162082156 39282801321 36536332719 197205718329
160 1339641765 1209415123 1952405387 974626813 4902953583
161 2439747269 867403835 3207377440 1447145063 3184539695
213 4542538577 1861026324 4550833326 3411151071 100580754
215 12501706224 7430813234 11656601640 11368063677 752026699
217 51172770366 14192262866 46162247492 34042506848 69737883006
223 6462172381 2515749859 4185148940 4548878338 344630890
249 28947231 42344256 47039768 25345595 278320079
STDs1_2_1 STDs1_3_1 STDs2_1_1 STDs2_2_1 STDs2_3_1
15 93755122107 145123990655 8.404316e+09 1.192403e+10 7.949020e+09
18 5697062448 10081537561 3.189715e+10 4.573937e+10 3.150348e+10
47 4374721588 4506276792 2.525499e+10 2.665673e+10 2.739119e+10
51 73977398769 81528685689 2.798814e+11 2.812251e+11 2.784481e+11
52 5283271185 6566022751 4.088573e+10 5.635563e+10 4.831191e+10
56 11963584450 13894114775 1.008694e+11 1.270551e+11 1.080933e+11
58 250205286119 296906572564 2.217792e+10 2.179285e+10 2.079125e+10
59 9872745569 13625947422 5.494318e+10 7.550947e+10 6.298413e+10
61 38711789699 26753642509 2.648382e+09 2.374563e+09 2.959823e+09
72 21761509473 24995275533 2.022219e+11 2.099681e+11 2.008734e+11
76 92471993196 111933034525 2.369427e+11 2.154171e+11 2.147613e+11
83 1404756223 1722349030 2.100855e+10 3.150182e+10 2.683373e+10
88 153609091820 194354374695 6.128364e+11 6.806437e+11 6.081936e+11
91 39740732153 52199463884 7.068595e+09 6.959272e+09 6.148607e+09
96 81478521606 90245103443 1.004679e+10 6.791705e+09 8.190063e+09
99 65484824893 78659013630 2.942373e+11 3.045492e+11 2.913047e+11
100 39973849685 52810194716 7.893543e+09 1.067456e+10 8.398831e+09
101 8031322337 11372950460 6.062762e+10 7.593066e+10 6.395370e+10
104 3377918987 4846034839 1.762278e+09 1.932329e+09 1.466095e+09
108 5908877444 6508543557 7.242981e+10 8.389181e+10 7.456268e+10
110 14912728474 15453555211 1.360954e+11 1.428008e+11 1.325633e+11
114 630455394604 691593486285 1.953280e+12 1.874967e+12 1.782247e+12
117 75872769034 84309471200 1.965054e+11 1.923675e+11 1.760045e+11
121 2292389898 2434361510 6.721220e+07 2.998448e+08 5.571211e+07
124 7941606634 12425549540 3.806126e+10 5.109673e+10 4.053765e+10
125 587338289 545705365 1.641202e+08 1.320211e+08 1.620409e+08
126 350631625 551431837 6.529316e+09 8.147023e+09 6.878607e+09
127 147306671523 174752895451 7.831476e+09 7.552937e+09 6.331847e+09
160 4214077038 5034225161 3.773436e+08 4.083171e+08 4.995101e+08
161 2253739082 3067220476 2.719207e+10 3.473551e+10 2.864230e+10
213 77790529 112175207 1.841030e+09 2.651612e+09 2.175243e+09
215 667422792 831898664 6.056732e+09 7.411239e+09 6.657432e+09
217 50355710853 74748728842 7.499197e+09 9.394351e+09 7.478331e+09
223 220999283 323169614 2.715179e+09 4.298793e+09 3.150293e+09
249 221576208 273784364 1.544969e+07 1.848276e+07 1.563547e+07
STDs3_1_1 STDs3_2_1 STDs3_3_1 STDs1_1_11 STDs1_2_11
15 52158906044 41528091695 47237120560 42800867054 31490919432
18 86958019135 67362753334 74008886448 13901294481 7519482898
47 2214789320 1954340597 1755736257 1779891940 10294177743
51 5644893474 6362735303 5521882730 29382190959 26095647360
52 66980204477 62619908572 66029114108 91535688370 80858868855
56 290012387636 252365638450 220762019380 10731071020 9362589517
58 167772454030 140395675493 126279496207 56788977986 49915424717
59 6461896227 5072746877 4625191078 27981851975 11556444546
61 5722104585 6343315631 5733731534 15683394808 5971671681
72 443323644017 402590116185 368125613272 14687482388 12287526320
76 15856891444 14016539510 10115998780 76805870704 64730847906
83 57438207477 47721748797 49203569830 9448295246 5806591020
88 32340027618 32913209103 23579898982 60023353685 42871997181
91 70599076199 58965144664 48713728179 24973672178 10084762101
96 43194374024 43244036759 34562666065 93755194438 87304675487
99 19584211218 17669849884 12860962107 50937864042 39479148815
100 32665710492 28164838177 26815625223 25732973590 23013737025
101 8822383126 7093756425 5454870255 3498150353 5263789509
104 15251961928 11337881946 10516557335 1596498743 649114020
108 190621325731 165402038092 156493074158 19897738488 14945218068
110 332061437484 302727826472 282002394563 97345693809 97910858320
114 167628663371 154342905192 119959546897 183153283732 160217487469
117 7190351635 6276096364 6092058765 176943112123 152897640734
121 2006530614 638777047 1797646794 4529859043 637063527
124 2335632866 1628373647 1839538048 15408259002 6442053700
125 545828923 504584069 451105832 581995497 13936787
126 28643916253 23016919959 21591637215 10755839164 105893539434
127 38408733412 41466932384 25908176232 55392718172 88648986592
160 2174818882 1976648176 1999123202 91408261 989468764
161 3799347369 3022722419 2223847599 1257793252 952238904
213 8389142186 6376326348 5592304607 259701557 198902971
215 13324917488 11489302785 11872781373 479975102 4239702376
217 90660559340 66495773118 56633232330 7958421257 4505414417
223 12441026942 9729753128 9295255432 43468003 13044846
249 46696910 42582740 58655048 5589994 4694366
STDs1_3_11 STDs2_1_11 STDs2_2_11 STDs2_3_11 STDs3_1_11
15 48629409467 2.328466e+10 3.110721e+10 59162804537 2.176074e+10
18 26077292529 1.667416e+10 2.692330e+09 60196815969 9.175921e+10
47 47518212949 2.467000e+08 8.301708e+09 8107188787 9.074667e+09
51 87963419807 8.075284e+10 8.563903e+10 30385906899 1.529216e+10
52 25718976207 2.523779e+09 5.749292e+09 66292796309 1.729819e+11
56 9831855561 8.424373e+10 1.416493e+11 274483027838 1.616161e+11
58 79497830826 1.873190e+11 1.324605e+11 181205249186 4.317583e+10
59 28740759209 2.273568e+09 2.810838e+10 17421538771 1.542499e+10
61 21511846495 2.958828e+09 3.105820e+09 3256663858 6.186081e+09
72 21428895487 2.570775e+11 8.697127e+10 241441583623 4.049046e+11
76 104564894397 2.488314e+11 1.120026e+11 254352394350 1.243827e+10
83 3028233104 3.885630e+09 1.283927e+10 88772806583 4.720201e+10
88 185387293072 1.943718e+11 2.474448e+11 89473005095 5.864948e+10
91 16815190937 7.080726e+09 3.012256e+10 12009902299 3.009008e+10
96 113423321385 3.217958e+09 3.284772e+09 3208579064 6.574794e+10
99 52466839323 5.593787e+10 1.328527e+11 41628382307 3.005319e+10
100 12295297787 9.215139e+09 1.723629e+10 501064941 9.309682e+10
101 548606920 5.650212e+12 3.012105e+13 1305198 1.196217e+12
104 1366159572 6.557767e+06 1.071380e+13 572032831753 1.231888e+09
108 23790434543 5.005457e+09 1.206172e+10 21881095649 4.066107e+11
110 105855997020 8.212865e+09 5.991087e+09 29607760550 9.933240e+11
114 551215167911 1.096709e+12 1.013756e+12 258125583771 2.122337e+11
117 299234030680 1.919773e+10 7.709080e+09 15529412242 2.585399e+10
121 6456123206 2.147082e+06 3.402262e+08 821799110 4.344733e+08
124 31251685244 2.332947e+09 2.705195e+09 3077948494 2.089187e+09
125 544320041 6.536052e+05 9.498233e+09 1263982 8.553710e+09
126 90668929197 4.126824e+06 4.030092e+05 348177892 1.235146e+11
127 152900163386 1.218678e+10 7.560132e+09 13152454640 3.033136e+10
160 1460417658 2.027069e+09 1.566245e+09 3181236365 3.628292e+08
161 17161367412 6.555336e+08 8.284932e+09 64267989 1.586791e+11
213 41941876 8.782536e+08 4.053647e+08 2774029981 3.055025e+09
215 4784197263 5.613618e+08 2.898819e+09 15022818163 2.957906e+10
217 14853899361 4.512733e+10 2.034344e+10 22704631391 1.551153e+10
223 2587757460 3.319342e+09 3.844441e+09 7419065422 1.026890e+10
249 1811188458 2.936097e+07 3.776329e+07 207482833 1.839774e+07
STDs3_2_11 STDs3_3_11
15 2.698957e+10 2.029999e+10
18 5.530783e+10 1.453166e+10
47 2.085176e+09 3.355313e+10
51 5.795141e+10 6.116596e+10
52 1.175251e+10 8.294444e+09
56 1.631644e+11 1.241299e+11
58 7.502429e+10 4.661585e+10
59 7.407526e+09 1.073086e+10
61 1.502941e+10 1.205702e+10
72 5.561003e+11 3.932784e+11
76 1.646239e+10 1.353549e+10
83 1.087941e+10 6.268587e+09
88 3.580872e+11 2.717819e+11
91 6.278069e+10 5.897435e+10
96 8.930133e+10 8.769464e+10
99 1.503650e+11 1.221974e+11
100 1.780190e+11 1.055258e+11
101 7.476378e+12 3.485990e+06
104 1.247234e+10 1.056943e+08
108 3.067219e+11 1.746252e+11
110 3.449097e+11 2.638215e+11
114 1.390537e+12 2.050180e+12
117 3.673642e+10 3.415640e+10
121 3.826636e+09 2.964771e+09
124 1.047505e+11 5.631976e+09
125 3.570236e+10 1.115516e+11
126 3.499914e+11 6.346830e+09
127 4.014473e+10 3.172141e+10
160 2.886765e+09 1.557802e+10
161 1.830826e+10 1.252431e+11
213 5.300128e+09 6.559798e+09
215 9.906880e+08 1.499178e+10
217 1.144314e+11 6.479159e+10
223 6.951225e+09 1.949586e+09
249 7.669666e+07 9.531366e+07
attr(,"scaled:center")
15 18 47 51 52 56 58 59
24.14313 23.82825 22.56031 24.51244 24.03559 24.96660 25.07258 23.35989
61 72 76 83 88 91 96 99
22.65701 25.53277 24.79739 23.28704 25.61284 23.80435 24.03270 24.89409
100 101 104 108 110 114 117 121
23.75712 23.49291 22.18672 24.51972 25.20350 26.96660 24.45338 20.36694
124 125 126 127 160 161 213 215
22.72807 20.02730 21.90146 24.09094 21.02939 22.44044 20.73831 22.15179
217 223 249
23.80154 21.20693 17.63491
attr(,"scaled:scale")
15 18 47 51 52 56 58 59
1.928955 2.377883 4.902530 1.905835 4.450198 2.920086 1.388851 5.334019
61 72 76 83 88 91 96 99
3.174722 1.585512 1.384230 5.662272 2.195056 3.761392 1.230772 2.728505
100 101 104 108 110 114 117 121
3.519278 5.716655 7.596538 3.530935 2.297653 1.207267 1.575265 3.343483
124 125 126 127 160 161 213 215
4.247852 5.945588 6.910316 1.446069 6.574229 6.653224 6.977456 4.594975
217 223 249
2.267837 3.401850 3.789944
crmn documentation built on March 26, 2020, 8:35 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Normalization methods for metabolomics data
Usage
1 |
Arguments
object |
an |
method |
the desired method |
segments |
normalization in a cross-validation setup, only to use for validation/QC purposes. |
... |
passed on to |
Details
Wrapper function for normFit and normPred
Value
the normalized dataset
Author(s)
Henning Redestig
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | data(mix)
normalize(mix, "crmn", factor="type", ncomp=3)
#other methods
normalize(mix, "one")
normalize(mix, "avg")
normalize(mix, "nomis")
normalize(mix, "t1")
normalize(mix, "ri")
normalize(mix, "median")
normalize(mix, "totL2")
## can also do normalization with matrices
Y <- exprs(mix)
G <- with(pData(mix), model.matrix(~-1+type))
isIS <- with(fData(mix), tag == "IS")
normalize(Y, "crmn", factor=G, ncomp=3, standards=isIS)
|
Example output
Loading required package: pcaMethods
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘pcaMethods’
The following object is masked from ‘package:stats’:
loadings
Attaching package: ‘crmn’
The following object is masked from ‘package:BiocGenerics’:
normalize
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 35 features, 42 samples
element names: exprs
protocolData: none
phenoData
sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
varLabels: type experiment runorder
varMetadata: labelDescription
featureData
featureNames: 15 18 ... 249 (35 total)
fvarLabels: mark tag ... preferred (7 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
STDs_1_2_1 STDs_1_2_2 STDs_1_2_3 STDs_1_3_1 STDs_1_3_2
15 42270693455 79813641464 62138560028 9.549550e+10 76956860360
18 1585976779 236918025 15768318093 1.116093e+10 73224501
47 3526793897 6135787546 4612524807 6.562883e+09 4099527809
51 28727285644 67217864436 44862206527 6.924001e+10 45671361861
52 4427597052 6763648607 5439439497 7.813281e+09 5396280421
56 7441691693 16566166368 10200900497 1.975485e+10 8779389559
58 140457728991 252393006147 173267295323 2.797450e+11 193302340239
59 5805487741 20699981668 8485729106 2.541731e+10 8851689536
61 16074447890 13914467888 11103652798 3.805633e+10 32510538205
72 8269615301 18023371096 9810547209 1.913980e+10 10568495046
76 50920341113 75365008959 54224254427 1.201478e+11 78695858855
83 1238038243 2846684989 1549350187 3.070157e+09 1483192392
88 55788988494 90945126632 55973565381 2.016199e+11 148544557540
91 27732966164 86302027892 34940201178 1.009936e+11 37364482053
96 63202595094 87685522620 99165764209 1.041214e+11 45429864674
99 37285155920 83401440694 45794828935 1.168215e+11 50066020875
100 25359841232 70113413225 22385741553 1.040998e+11 42863275353
101 6267398512 29118203394 12993724464 4.073640e+10 8992758261
104 2390335230 15206635497 3937922974 2.086045e+10 4409278084
108 5551637784 10289231741 5050698802 1.399565e+10 5548696252
110 15467394112 20289432548 16017717035 2.835453e+10 13933559364
114 402402513497 667212999322 433710121382 1.145646e+12 438282862583
117 44235363372 60432776558 36339400913 1.303982e+11 63146254189
121 2350846248 2383121627 1848696689 1.834055e+10 1870734025
124 3465334679 6248822882 3878625721 2.860431e+10 7861423352
125 701317456 801751534 380424083 1.500798e+09 1005196964
126 246202662 592787893 279904898 1.085224e+09 248966223
127 91563022237 122333359163 93487387514 2.424798e+11 80631388016
160 1723814957 3258106689 1715185887 7.097407e+09 2638375170
161 949809418 5228203453 1074765504 1.628670e+10 1736445177
213 39130162 128332965 82901657 2.495666e+08 58733636
215 489950720 942143485 842280831 1.036102e+09 577197578
217 15158366384 85010379317 33253559529 1.066290e+11 24705763766
223 117026248 468261788 203050408 7.359517e+08 161616949
249 107813980 96171889 58875955 2.440207e+08 180093177
STDs_1_3_3 STDs_2_1_1 STDs_2_1_2 STDs_2_1_3 STDs_2_2_1
15 75010783749 9.555348e+09 7.134046e+09 6.853384e+09 7.034869e+09
18 21681359180 2.761876e+10 1.950810e+10 8.948037e+10 2.933949e+10
47 5423063600 2.520831e+10 1.851556e+10 2.349083e+10 1.922214e+10
51 57656993568 2.071207e+11 1.422851e+11 1.996128e+11 1.517924e+11
52 6135985161 3.990635e+10 4.005675e+10 3.868305e+10 3.634357e+10
56 13523567647 9.082425e+10 7.328525e+10 8.179510e+10 6.958371e+10
58 211755827412 2.100347e+10 1.534581e+10 1.446463e+10 1.534828e+10
59 13950873794 4.940696e+10 4.053220e+10 4.742963e+10 3.404221e+10
61 12327451421 3.332152e+09 2.112612e+09 1.741369e+09 2.263492e+09
72 13543347065 1.803916e+11 1.450110e+11 1.971707e+11 1.419434e+11
76 63414736898 2.338107e+11 1.585346e+11 2.338519e+11 1.759188e+11
83 2102283783 1.802098e+10 1.644348e+10 1.988222e+10 1.425008e+10
88 81074143552 7.254881e+11 4.950776e+11 6.609316e+11 4.937580e+11
91 54214119701 7.161547e+09 4.704187e+09 3.912173e+09 4.760500e+09
96 39612521217 1.208625e+10 7.691634e+09 6.816257e+09 8.716165e+09
99 63214107525 2.377051e+11 1.559830e+11 1.958846e+11 1.652958e+11
100 33752487630 1.180161e+10 7.370869e+09 4.952936e+09 8.376151e+09
101 22886317954 5.968560e+10 3.822043e+10 5.578889e+10 3.591506e+10
104 8382669159 1.693421e+09 1.223522e+09 1.276877e+09 1.047175e+09
108 7135998235 6.766793e+10 4.517514e+10 5.533502e+10 5.093137e+10
110 19553088628 1.190313e+11 8.067676e+10 1.086343e+11 9.799135e+10
114 635139161914 1.632465e+12 1.001129e+12 1.587189e+12 1.194458e+12
117 43774621877 2.142720e+11 1.370798e+11 1.709833e+11 1.846162e+11
121 2154380628 4.572226e+08 7.679945e+07 9.602150e+07 1.790931e+08
124 6087442089 7.665869e+10 3.826853e+10 6.992107e+10 5.083174e+10
125 423602799 1.296620e+09 4.383309e+08 6.796225e+07 1.087719e+09
126 457232955 4.867662e+09 2.312149e+09 3.250615e+09 3.207918e+09
127 116218226910 7.775563e+09 4.373757e+09 5.547087e+09 7.822436e+09
160 2695383526 1.125607e+09 3.787050e+08 5.062768e+08 9.726216e+08
161 2735460570 2.873677e+10 1.137963e+10 2.321683e+10 1.503062e+10
213 151719923 1.484724e+09 1.049124e+09 1.357375e+09 9.210870e+08
215 1106069945 5.454540e+09 5.141207e+09 6.311006e+09 4.581682e+09
217 66859570482 5.003973e+09 3.812508e+09 5.663840e+09 2.963841e+09
223 367729514 1.735860e+09 1.045057e+09 1.661789e+09 1.062922e+09
249 82096366 2.457915e+07 1.664941e+07 1.933582e+07 2.461825e+07
STDs_2_2_2 STDs_2_2_3 STDs_2_3_1 STDs_2_3_2 STDs_2_3_3
15 1.004828e+10 6.241870e+09 1.010163e+10 9.831291e+09 8.403516e+09
18 4.137106e+09 7.773814e+10 5.576874e+10 7.877096e+09 1.410028e+11
47 2.806378e+10 2.062458e+10 2.470496e+10 2.671047e+10 2.733098e+10
51 2.322868e+11 1.792538e+11 2.051970e+11 2.221660e+11 2.320415e+11
52 4.526602e+10 3.739765e+10 4.204741e+10 4.611995e+10 4.668027e+10
56 1.074974e+11 7.361460e+10 9.652446e+10 1.062041e+11 1.031245e+11
58 2.275979e+10 1.309482e+10 2.110163e+10 2.165548e+10 1.827739e+10
59 6.518585e+10 4.124044e+10 5.881808e+10 6.832425e+10 6.317563e+10
61 3.067962e+09 1.572813e+09 3.550440e+09 2.905126e+09 1.789692e+09
72 2.090836e+11 1.869965e+11 1.906256e+11 1.988704e+11 2.486657e+11
76 2.383028e+11 2.118971e+11 2.420150e+11 2.252833e+11 2.661898e+11
83 2.187930e+10 1.852608e+10 1.988835e+10 2.169279e+10 2.502001e+10
88 8.343073e+11 6.016269e+11 8.204417e+11 8.036685e+11 7.493921e+11
91 7.875875e+09 3.304762e+09 8.102287e+09 7.293070e+09 5.926175e+09
96 1.037039e+10 9.318858e+09 1.104407e+10 4.244209e+09 1.157301e+10
99 2.528343e+11 1.749558e+11 2.567638e+11 2.422465e+11 2.365353e+11
100 1.230937e+10 4.397820e+09 1.376289e+10 1.169404e+10 6.082376e+09
101 7.755080e+10 4.800951e+10 7.279799e+10 7.516272e+10 7.657146e+10
104 2.612365e+09 1.111437e+09 2.336324e+09 2.428709e+09 1.826664e+09
108 6.664684e+10 4.927776e+10 7.277440e+10 6.197013e+10 6.418220e+10
110 1.072021e+11 1.019515e+11 1.218898e+11 9.830618e+10 1.243989e+11
114 1.582232e+12 1.441088e+12 1.749609e+12 1.513251e+12 1.704714e+12
117 1.908377e+11 1.610008e+11 2.487462e+11 1.752054e+11 1.949258e+11
121 1.302160e+08 1.731239e+08 3.157305e+08 1.469368e+08 5.970648e+07
124 7.048831e+10 5.741248e+10 1.056301e+11 7.504254e+10 9.402054e+10
125 7.679793e+08 3.897844e+07 1.365416e+09 7.088795e+08 1.287430e+08
126 3.898400e+09 2.569002e+09 5.911560e+09 3.720173e+09 4.155117e+09
127 6.721401e+09 5.002176e+09 9.775062e+09 5.566900e+09 5.665427e+09
160 5.770342e+08 1.730097e+08 1.630580e+09 5.924180e+08 6.386275e+08
161 2.943782e+10 1.687650e+10 3.708756e+10 2.862992e+10 3.410166e+10
213 1.687643e+09 1.089441e+09 1.765339e+09 1.895280e+09 1.918399e+09
215 6.367717e+09 6.030505e+09 5.957383e+09 6.787141e+09 7.412499e+09
217 7.011393e+09 4.871120e+09 6.353766e+09 7.488186e+09 8.688316e+09
223 1.883053e+09 1.233549e+09 2.324103e+09 1.829068e+09 2.054823e+09
249 2.264114e+07 1.704520e+07 2.924462e+07 2.068004e+07 1.490853e+07
STDs_3_1_1 STDs_3_1_2 STDs_3_1_3 STDs_3_2_1 STDs_3_2_2
15 32129302305 69629740623 58510814230 35711882800 73819842388
18 33096458970 50997159141 301622847945 33639050108 50238064145
47 1712669075 2930969833 1814221054 1873341261 2928058313
51 5929716543 11598048699 7017055274 6394483611 12700014233
52 47209386445 76336154688 65717466511 48962520675 80407473837
56 129523642350 302973504134 223892840431 139091044535 314216389909
58 96760635409 186061334931 141651087869 103292791306 192402571847
59 2045276218 7751395656 4241261796 2295214784 8216346472
61 7710348409 12957731987 6283148863 7261319971 14509013418
72 266609635932 546970727979 497879066310 283847989820 552132244814
76 10358738158 15660722408 11190247857 10973108482 15577397750
83 22851423276 52743156363 46947495110 24603428024 54714247996
88 19763671299 46659584609 27915224737 21705932854 54861363270
91 22482914712 67545252776 43500643322 24444722993 74502180270
96 36449892521 46905043748 32075906566 38934878209 47267864522
99 12602199654 28130032621 19547351553 14021083262 29423116745
100 16126681399 47840386404 30619527539 17564191202 51302602003
101 1822513349 9484150025 4423348010 2236706681 9099639207
104 3754169789 25718536702 12584261918 4408325951 24767982450
108 97773325287 176352564650 144604480263 105875352191 181763710039
110 200147882325 262204979628 263149725218 208928170440 264367466829
114 120757101551 198564124041 138203711636 133718216818 206140969476
117 6336406351 8883066504 5325643001 6544936971 9200050518
121 1284927850 2227923023 500641901 972028316 994019599
124 529029210 771687411 897999355 474893442 902318318
125 1045898597 945009869 432752054 1132216979 1001561124
126 6350083101 13442399497 13359369669 7250404489 14282851587
127 37325385374 50384884807 46041803903 41560342985 34681537100
160 1279684574 2219432896 1393337412 1365738115 2445925732
161 782677912 5311331743 2530055042 924022667 6532515157
213 1694417817 7361730179 5207003124 1922042917 8517724633
215 7067311580 14401715220 14184376790 7498269069 15029566028
217 12134343059 77327854079 54515133266 13983791410 83880522741
223 2382871412 7360424984 8612411951 2713624608 8403600946
249 47210237 43703857 34856492 48290249 47436771
STDs_3_2_3 STDs_3_3_1 STDs_3_3_2 STDs_3_3_3 STDs1_1_1
15 64417603554 35510859891 62131428503 58819970598 112507642440
18 201410244088 25921151660 39458222895 192335643569 6898383871
47 2088809374 1839922659 2617343958 2061344247 3830288544
51 7636731941 6633910914 11364750713 6570088204 70400029787
52 59123740044 47507007667 66568444106 56191917913 5576899002
56 222492074712 134101237145 240412107271 191744239883 12912248564
58 160405864930 101486445365 165360986695 138425098586 267941894524
59 4194380924 2291844562 5365817379 3217037241 12328431439
61 6711329901 7011295204 12785890231 5988188477 30936857243
72 515472733230 271787257341 460580285264 438160627049 27230148140
76 11969120235 10518400230 13570236516 10460792072 102162409624
83 42356300421 24204892290 41480892348 36140501879 1882892883
88 29765133738 21379425997 40421694160 23627097043 185195802466
91 44513363860 23698765659 50225173756 32470049055 50908356303
96 48668321631 19146612138 43881789918 49926557990 87767490106
99 22016080837 13503821135 22692571437 17950156049 77804551670
100 32163775216 16678864127 36145529889 23925678384 51575451535
101 5093928789 1913077177 6243586520 3476066219 11033121629
104 12937421578 4164355821 14708997735 7345562309 5065021939
108 132692591465 103024512441 142819816186 111283741940 7421050806
110 252988704437 200327089965 231448930494 226038579119 17988656469
114 145152249542 128824397953 168155288670 121836028676 739281202177
117 5207976701 6162991230 8053998551 3997279349 97945029117
121 1704958496 1441243166 585663575 700726818 9866325871
124 773409670 471633420 665623851 555857068 11947631874
125 463729069 1031149833 1036802853 383229027 620047630
126 11535543907 6927943873 8612073459 8588256555 495192441
127 47780402428 31162082156 39282801321 36536332719 197205718329
160 1339641765 1209415123 1952405387 974626813 4902953583
161 2439747269 867403835 3207377440 1447145063 3184539695
213 4542538577 1861026324 4550833326 3411151071 100580754
215 12501706224 7430813234 11656601640 11368063677 752026699
217 51172770366 14192262866 46162247492 34042506848 69737883006
223 6462172381 2515749859 4185148940 4548878338 344630890
249 28947231 42344256 47039768 25345595 278320079
STDs1_2_1 STDs1_3_1 STDs2_1_1 STDs2_2_1 STDs2_3_1
15 93755122107 145123990655 8.404316e+09 1.192403e+10 7.949020e+09
18 5697062448 10081537561 3.189715e+10 4.573937e+10 3.150348e+10
47 4374721588 4506276792 2.525499e+10 2.665673e+10 2.739119e+10
51 73977398769 81528685689 2.798814e+11 2.812251e+11 2.784481e+11
52 5283271185 6566022751 4.088573e+10 5.635563e+10 4.831191e+10
56 11963584450 13894114775 1.008694e+11 1.270551e+11 1.080933e+11
58 250205286119 296906572564 2.217792e+10 2.179285e+10 2.079125e+10
59 9872745569 13625947422 5.494318e+10 7.550947e+10 6.298413e+10
61 38711789699 26753642509 2.648382e+09 2.374563e+09 2.959823e+09
72 21761509473 24995275533 2.022219e+11 2.099681e+11 2.008734e+11
76 92471993196 111933034525 2.369427e+11 2.154171e+11 2.147613e+11
83 1404756223 1722349030 2.100855e+10 3.150182e+10 2.683373e+10
88 153609091820 194354374695 6.128364e+11 6.806437e+11 6.081936e+11
91 39740732153 52199463884 7.068595e+09 6.959272e+09 6.148607e+09
96 81478521606 90245103443 1.004679e+10 6.791705e+09 8.190063e+09
99 65484824893 78659013630 2.942373e+11 3.045492e+11 2.913047e+11
100 39973849685 52810194716 7.893543e+09 1.067456e+10 8.398831e+09
101 8031322337 11372950460 6.062762e+10 7.593066e+10 6.395370e+10
104 3377918987 4846034839 1.762278e+09 1.932329e+09 1.466095e+09
108 5908877444 6508543557 7.242981e+10 8.389181e+10 7.456268e+10
110 14912728474 15453555211 1.360954e+11 1.428008e+11 1.325633e+11
114 630455394604 691593486285 1.953280e+12 1.874967e+12 1.782247e+12
117 75872769034 84309471200 1.965054e+11 1.923675e+11 1.760045e+11
121 2292389898 2434361510 6.721220e+07 2.998448e+08 5.571211e+07
124 7941606634 12425549540 3.806126e+10 5.109673e+10 4.053765e+10
125 587338289 545705365 1.641202e+08 1.320211e+08 1.620409e+08
126 350631625 551431837 6.529316e+09 8.147023e+09 6.878607e+09
127 147306671523 174752895451 7.831476e+09 7.552937e+09 6.331847e+09
160 4214077038 5034225161 3.773436e+08 4.083171e+08 4.995101e+08
161 2253739082 3067220476 2.719207e+10 3.473551e+10 2.864230e+10
213 77790529 112175207 1.841030e+09 2.651612e+09 2.175243e+09
215 667422792 831898664 6.056732e+09 7.411239e+09 6.657432e+09
217 50355710853 74748728842 7.499197e+09 9.394351e+09 7.478331e+09
223 220999283 323169614 2.715179e+09 4.298793e+09 3.150293e+09
249 221576208 273784364 1.544969e+07 1.848276e+07 1.563547e+07
STDs3_1_1 STDs3_2_1 STDs3_3_1 STDs1_1_11 STDs1_2_11
15 52158906044 41528091695 47237120560 42800867054 31490919432
18 86958019135 67362753334 74008886448 13901294481 7519482898
47 2214789320 1954340597 1755736257 1779891940 10294177743
51 5644893474 6362735303 5521882730 29382190959 26095647360
52 66980204477 62619908572 66029114108 91535688370 80858868855
56 290012387636 252365638450 220762019380 10731071020 9362589517
58 167772454030 140395675493 126279496207 56788977986 49915424717
59 6461896227 5072746877 4625191078 27981851975 11556444546
61 5722104585 6343315631 5733731534 15683394808 5971671681
72 443323644017 402590116185 368125613272 14687482388 12287526320
76 15856891444 14016539510 10115998780 76805870704 64730847906
83 57438207477 47721748797 49203569830 9448295246 5806591020
88 32340027618 32913209103 23579898982 60023353685 42871997181
91 70599076199 58965144664 48713728179 24973672178 10084762101
96 43194374024 43244036759 34562666065 93755194438 87304675487
99 19584211218 17669849884 12860962107 50937864042 39479148815
100 32665710492 28164838177 26815625223 25732973590 23013737025
101 8822383126 7093756425 5454870255 3498150353 5263789509
104 15251961928 11337881946 10516557335 1596498743 649114020
108 190621325731 165402038092 156493074158 19897738488 14945218068
110 332061437484 302727826472 282002394563 97345693809 97910858320
114 167628663371 154342905192 119959546897 183153283732 160217487469
117 7190351635 6276096364 6092058765 176943112123 152897640734
121 2006530614 638777047 1797646794 4529859043 637063527
124 2335632866 1628373647 1839538048 15408259002 6442053700
125 545828923 504584069 451105832 581995497 13936787
126 28643916253 23016919959 21591637215 10755839164 105893539434
127 38408733412 41466932384 25908176232 55392718172 88648986592
160 2174818882 1976648176 1999123202 91408261 989468764
161 3799347369 3022722419 2223847599 1257793252 952238904
213 8389142186 6376326348 5592304607 259701557 198902971
215 13324917488 11489302785 11872781373 479975102 4239702376
217 90660559340 66495773118 56633232330 7958421257 4505414417
223 12441026942 9729753128 9295255432 43468003 13044846
249 46696910 42582740 58655048 5589994 4694366
STDs1_3_11 STDs2_1_11 STDs2_2_11 STDs2_3_11 STDs3_1_11
15 48629409467 2.328466e+10 3.110721e+10 59162804537 2.176074e+10
18 26077292529 1.667416e+10 2.692330e+09 60196815969 9.175921e+10
47 47518212949 2.467000e+08 8.301708e+09 8107188787 9.074667e+09
51 87963419807 8.075284e+10 8.563903e+10 30385906899 1.529216e+10
52 25718976207 2.523779e+09 5.749292e+09 66292796309 1.729819e+11
56 9831855561 8.424373e+10 1.416493e+11 274483027838 1.616161e+11
58 79497830826 1.873190e+11 1.324605e+11 181205249186 4.317583e+10
59 28740759209 2.273568e+09 2.810838e+10 17421538771 1.542499e+10
61 21511846495 2.958828e+09 3.105820e+09 3256663858 6.186081e+09
72 21428895487 2.570775e+11 8.697127e+10 241441583623 4.049046e+11
76 104564894397 2.488314e+11 1.120026e+11 254352394350 1.243827e+10
83 3028233104 3.885630e+09 1.283927e+10 88772806583 4.720201e+10
88 185387293072 1.943718e+11 2.474448e+11 89473005095 5.864948e+10
91 16815190937 7.080726e+09 3.012256e+10 12009902299 3.009008e+10
96 113423321385 3.217958e+09 3.284772e+09 3208579064 6.574794e+10
99 52466839323 5.593787e+10 1.328527e+11 41628382307 3.005319e+10
100 12295297787 9.215139e+09 1.723629e+10 501064941 9.309682e+10
101 548606920 5.650212e+12 3.012105e+13 1305198 1.196217e+12
104 1366159572 6.557767e+06 1.071380e+13 572032831753 1.231888e+09
108 23790434543 5.005457e+09 1.206172e+10 21881095649 4.066107e+11
110 105855997020 8.212865e+09 5.991087e+09 29607760550 9.933240e+11
114 551215167911 1.096709e+12 1.013756e+12 258125583771 2.122337e+11
117 299234030680 1.919773e+10 7.709080e+09 15529412242 2.585399e+10
121 6456123206 2.147082e+06 3.402262e+08 821799110 4.344733e+08
124 31251685244 2.332947e+09 2.705195e+09 3077948494 2.089187e+09
125 544320041 6.536052e+05 9.498233e+09 1263982 8.553710e+09
126 90668929197 4.126824e+06 4.030092e+05 348177892 1.235146e+11
127 152900163386 1.218678e+10 7.560132e+09 13152454640 3.033136e+10
160 1460417658 2.027069e+09 1.566245e+09 3181236365 3.628292e+08
161 17161367412 6.555336e+08 8.284932e+09 64267989 1.586791e+11
213 41941876 8.782536e+08 4.053647e+08 2774029981 3.055025e+09
215 4784197263 5.613618e+08 2.898819e+09 15022818163 2.957906e+10
217 14853899361 4.512733e+10 2.034344e+10 22704631391 1.551153e+10
223 2587757460 3.319342e+09 3.844441e+09 7419065422 1.026890e+10
249 1811188458 2.936097e+07 3.776329e+07 207482833 1.839774e+07
STDs3_2_11 STDs3_3_11
15 2.698957e+10 2.029999e+10
18 5.530783e+10 1.453166e+10
47 2.085176e+09 3.355313e+10
51 5.795141e+10 6.116596e+10
52 1.175251e+10 8.294444e+09
56 1.631644e+11 1.241299e+11
58 7.502429e+10 4.661585e+10
59 7.407526e+09 1.073086e+10
61 1.502941e+10 1.205702e+10
72 5.561003e+11 3.932784e+11
76 1.646239e+10 1.353549e+10
83 1.087941e+10 6.268587e+09
88 3.580872e+11 2.717819e+11
91 6.278069e+10 5.897435e+10
96 8.930133e+10 8.769464e+10
99 1.503650e+11 1.221974e+11
100 1.780190e+11 1.055258e+11
101 7.476378e+12 3.485990e+06
104 1.247234e+10 1.056943e+08
108 3.067219e+11 1.746252e+11
110 3.449097e+11 2.638215e+11
114 1.390537e+12 2.050180e+12
117 3.673642e+10 3.415640e+10
121 3.826636e+09 2.964771e+09
124 1.047505e+11 5.631976e+09
125 3.570236e+10 1.115516e+11
126 3.499914e+11 6.346830e+09
127 4.014473e+10 3.172141e+10
160 2.886765e+09 1.557802e+10
161 1.830826e+10 1.252431e+11
213 5.300128e+09 6.559798e+09
215 9.906880e+08 1.499178e+10
217 1.144314e+11 6.479159e+10
223 6.951225e+09 1.949586e+09
249 7.669666e+07 9.531366e+07
attr(,"scaled:center")
15 18 47 51 52 56 58 59
24.14313 23.82825 22.56031 24.51244 24.03559 24.96660 25.07258 23.35989
61 72 76 83 88 91 96 99
22.65701 25.53277 24.79739 23.28704 25.61284 23.80435 24.03270 24.89409
100 101 104 108 110 114 117 121
23.75712 23.49291 22.18672 24.51972 25.20350 26.96660 24.45338 20.36694
124 125 126 127 160 161 213 215
22.72807 20.02730 21.90146 24.09094 21.02939 22.44044 20.73831 22.15179
217 223 249
23.80154 21.20693 17.63491
attr(,"scaled:scale")
15 18 47 51 52 56 58 59
1.928955 2.377883 4.902530 1.905835 4.450198 2.920086 1.388851 5.334019
61 72 76 83 88 91 96 99
3.174722 1.585512 1.384230 5.662272 2.195056 3.761392 1.230772 2.728505
100 101 104 108 110 114 117 121
3.519278 5.716655 7.596538 3.530935 2.297653 1.207267 1.575265 3.343483
124 125 126 127 160 161 213 215
4.247852 5.945588 6.910316 1.446069 6.574229 6.653224 6.977456 4.594975
217 223 249
2.267837 3.401850 3.789944
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