bestKeeper: Determines stability of genes
In ctrlGene: Assess the Stability of Candidate Housekeeping Genes
Description
Usage
Arguments
Value
References
Examples
Description
This function combines the results of cpSta(), pearsonCor() and bki().
Usage
1
bestKeeper(expression, ctVal = TRUE)
Arguments
expression
a matrix of expression levels. Each row corresponds to a sample and each column to a gene.
ctVal
a logical value indicating data type. If ct-values are input, ctVal=TRUE, otherwise, ctVal=FALSE.
Value
A list containing CP.statistics, pair.Wise.cor and HKG.vs.BestKeeper, which are returned by cpSta(), pearsonCor() and bki(), respectively.
References
Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Biotechnol Lett (2004) <doi: 10.1023/B:BILE.0000019559.84305.47>
Examples
1
2
Example output
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
FIB1 19.00201 19.60900 18.95384 19.71017 19.05019 19.57528 19.34405 19.18989
FIB2 20.06665 19.06464 19.79688 21.11202 19.67163 20.06183 19.99439 20.08110
FIB3 19.93177 19.06464 20.63510 21.48296 20.76035 19.87396 20.05220 20.42314
FIB4 20.72663 18.00000 19.11281 20.26416 19.81133 19.84987 19.41149 21.11684
FIB5 18.55882 18.73706 18.52509 19.58010 18.38539 18.78041 18.85267 18.31795
FIB6 30.61144 27.38419 27.76968 25.39467 28.35244 27.33128 28.06352 31.34360
FIB7 18.79968 18.76114 19.03573 19.47893 18.96347 19.19953 19.18989 18.80450
FIB8 20.44241 19.04537 20.37496 21.69492 20.72181 18.65998 20.89524 21.20355
FIB9 19.83060 18.77078 19.34405 20.85670 19.37295 19.06464 19.39222 19.60900
FIB10 25.50546 24.28666 24.39265 25.34649 24.73469 23.62187 23.94463 24.81177
FIB11 24.94665 23.42918 23.89165 23.89165 24.18551 22.36454 22.55723 24.49864
FIB12 24.12770 23.36655 24.49864 24.86957 24.39265 23.00525 22.67285 24.18551
FIB13 25.12970 24.08916 24.88883 25.06709 24.69133 23.84829 23.64596 25.37057
FIB14 18.52028 19.16099 18.75151 19.02128 18.67925 18.89121 18.84786 18.84304
FIB15 20.34606 20.94341 19.81615 21.00122 20.19672 19.73907 20.25935 20.41350
FIB16 19.23806 21.40106 18.80450 19.58973 18.87676 19.33923 19.34405 19.85469
FIB17 18.01445 18.47210 18.47210 18.65998 18.18788 18.92975 18.18306 18.26014
FIB18 18.98756 18.91048 18.95866 19.12726 18.90567 18.74669 19.14172 18.97793
FIB19 18.00000 18.46247 18.00000 18.00000 18.00000 18.00000 18.00000 18.00000
FIB20 19.66199 20.15336 19.32478 19.97512 19.81615 19.75352 19.38259 19.57528
UBC YWHAZ
FIB1 19.16099 18.80450
FIB2 20.17263 19.50784
FIB3 20.49058 19.70535
FIB4 19.42594 20.17263
FIB5 18.80450 18.23123
FIB6 29.37391 28.50195
FIB7 19.25733 18.54436
FIB8 20.46168 20.55802
FIB9 19.28142 19.54638
FIB10 24.59980 24.33966
FIB11 23.47253 23.39064
FIB12 23.81938 24.01689
FIB13 24.56126 24.13733
FIB14 18.86231 18.49619
FIB15 19.16580 20.09074
FIB16 19.27179 18.92012
FIB17 18.18306 18.02409
FIB18 18.76114 19.09836
FIB19 18.00000 18.00000
FIB20 19.18026 19.51747
$CP.statistics
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
N 20.000 20.000 20.000 20.000 20.000 20.000 20.000 20.000
GM[CP] 20.805 20.413 20.506 21.083 20.617 20.314 20.433 20.927
AM[CP] 21.022 20.556 20.667 21.206 20.788 20.432 20.559 21.144
Min[CP] 18.000 18.000 18.000 18.000 18.000 18.000 18.000 18.000
Max[CP] 30.611 27.384 27.770 25.395 28.352 27.331 28.064 31.344
SD[+/- CP] 2.521 2.101 2.210 1.930 2.242 1.801 1.843 2.455
CV[%CP] 11.991 10.222 10.695 9.103 10.784 8.816 8.963 11.611
Min[x-fold] -6.989 -5.326 -5.679 -8.472 -6.134 -4.974 -5.399 -7.605
Max[x-fold] 895.323 125.453 153.711 19.862 213.149 129.505 198.218 1366.877
SD[+/- x-fold] 5.739 4.290 4.628 3.812 4.730 3.485 3.587 5.483
UBC YWHAZ
N 20.000 20.000
GM[CP] 20.542 20.417
AM[CP] 20.715 20.580
Min[CP] 18.000 18.000
Max[CP] 29.374 28.502
SD[+/- CP] 2.225 2.149
CV[%CP] 10.741 10.440
Min[x-fold] -5.823 -5.341
Max[x-fold] 455.742 271.510
SD[+/- x-fold] 4.675 4.434
$pair.Wise.cor
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP UBC YWHAZ
B2M 0.936 1.000 0.937 0.870 0.935 0.947 0.937 0.927 0.934 0.934
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
GAPD 0.979 0.937 1.000 0.959 0.996 0.970 0.975 0.971 0.986 0.985
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
HMBS 0.925 0.870 0.959 1.000 0.956 0.903 0.920 0.907 0.925 0.937
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
HPRT1 0.988 0.935 0.996 0.956 1.000 0.970 0.982 0.982 0.987 0.993
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
RPL13A 0.978 0.947 0.970 0.903 0.970 1.000 0.969 0.971 0.980 0.972
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
SDHA 0.987 0.937 0.975 0.920 0.982 0.969 1.000 0.988 0.991 0.987
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
TBP 0.994 0.927 0.971 0.907 0.982 0.971 0.988 1.000 0.986 0.991
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
UBC 0.987 0.934 0.986 0.925 0.987 0.980 0.991 0.986 1.000 0.986
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
YWHAZ 0.995 0.934 0.985 0.937 0.993 0.972 0.987 0.991 0.986 1.000
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
$HKG.vs.BestKeeper
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
coeff. of corr. [r] 0.994 0.951 0.993 0.945 0.996 0.983 0.990 0.989
coeff. of det. [r^2] 0.989 0.905 0.985 0.893 0.992 0.965 0.981 0.979
intercept [CP] -3.934 1.826 -0.318 3.959 -0.933 2.778 1.994 -3.861
slope [CP] 1.202 0.902 1.011 0.831 1.046 0.850 0.894 1.205
SE [CP] 0.361 0.822 0.348 0.805 0.268 0.451 0.349 0.498
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Power [x-fold] 2.301 1.869 2.015 1.779 2.065 1.803 1.859 2.305
UBC YWHAZ
coeff. of corr. [r] 0.993 0.995
coeff. of det. [r^2] 0.987 0.991
intercept [CP] -1.354 -0.616
slope [CP] 1.063 1.021
SE [CP] 0.348 0.277
p-value 0.000 0.000
Power [x-fold] 2.090 2.029
ctrlGene documentation built on July 4, 2019, 5:05 p.m.
R Package Documentation
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Description Usage Arguments Value References Examples
Description
This function combines the results of cpSta(), pearsonCor() and bki().
Usage
1 | bestKeeper(expression, ctVal = TRUE)
|
Arguments
expression |
a matrix of expression levels. Each row corresponds to a sample and each column to a gene. |
ctVal |
a logical value indicating data type. If ct-values are input, ctVal=TRUE, otherwise, ctVal=FALSE. |
Value
A list containing CP.statistics, pair.Wise.cor and HKG.vs.BestKeeper, which are returned by cpSta(), pearsonCor() and bki(), respectively.
References
Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Biotechnol Lett (2004) <doi: 10.1023/B:BILE.0000019559.84305.47>
Examples
1 2 |
Example output
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
FIB1 19.00201 19.60900 18.95384 19.71017 19.05019 19.57528 19.34405 19.18989
FIB2 20.06665 19.06464 19.79688 21.11202 19.67163 20.06183 19.99439 20.08110
FIB3 19.93177 19.06464 20.63510 21.48296 20.76035 19.87396 20.05220 20.42314
FIB4 20.72663 18.00000 19.11281 20.26416 19.81133 19.84987 19.41149 21.11684
FIB5 18.55882 18.73706 18.52509 19.58010 18.38539 18.78041 18.85267 18.31795
FIB6 30.61144 27.38419 27.76968 25.39467 28.35244 27.33128 28.06352 31.34360
FIB7 18.79968 18.76114 19.03573 19.47893 18.96347 19.19953 19.18989 18.80450
FIB8 20.44241 19.04537 20.37496 21.69492 20.72181 18.65998 20.89524 21.20355
FIB9 19.83060 18.77078 19.34405 20.85670 19.37295 19.06464 19.39222 19.60900
FIB10 25.50546 24.28666 24.39265 25.34649 24.73469 23.62187 23.94463 24.81177
FIB11 24.94665 23.42918 23.89165 23.89165 24.18551 22.36454 22.55723 24.49864
FIB12 24.12770 23.36655 24.49864 24.86957 24.39265 23.00525 22.67285 24.18551
FIB13 25.12970 24.08916 24.88883 25.06709 24.69133 23.84829 23.64596 25.37057
FIB14 18.52028 19.16099 18.75151 19.02128 18.67925 18.89121 18.84786 18.84304
FIB15 20.34606 20.94341 19.81615 21.00122 20.19672 19.73907 20.25935 20.41350
FIB16 19.23806 21.40106 18.80450 19.58973 18.87676 19.33923 19.34405 19.85469
FIB17 18.01445 18.47210 18.47210 18.65998 18.18788 18.92975 18.18306 18.26014
FIB18 18.98756 18.91048 18.95866 19.12726 18.90567 18.74669 19.14172 18.97793
FIB19 18.00000 18.46247 18.00000 18.00000 18.00000 18.00000 18.00000 18.00000
FIB20 19.66199 20.15336 19.32478 19.97512 19.81615 19.75352 19.38259 19.57528
UBC YWHAZ
FIB1 19.16099 18.80450
FIB2 20.17263 19.50784
FIB3 20.49058 19.70535
FIB4 19.42594 20.17263
FIB5 18.80450 18.23123
FIB6 29.37391 28.50195
FIB7 19.25733 18.54436
FIB8 20.46168 20.55802
FIB9 19.28142 19.54638
FIB10 24.59980 24.33966
FIB11 23.47253 23.39064
FIB12 23.81938 24.01689
FIB13 24.56126 24.13733
FIB14 18.86231 18.49619
FIB15 19.16580 20.09074
FIB16 19.27179 18.92012
FIB17 18.18306 18.02409
FIB18 18.76114 19.09836
FIB19 18.00000 18.00000
FIB20 19.18026 19.51747
$CP.statistics
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
N 20.000 20.000 20.000 20.000 20.000 20.000 20.000 20.000
GM[CP] 20.805 20.413 20.506 21.083 20.617 20.314 20.433 20.927
AM[CP] 21.022 20.556 20.667 21.206 20.788 20.432 20.559 21.144
Min[CP] 18.000 18.000 18.000 18.000 18.000 18.000 18.000 18.000
Max[CP] 30.611 27.384 27.770 25.395 28.352 27.331 28.064 31.344
SD[+/- CP] 2.521 2.101 2.210 1.930 2.242 1.801 1.843 2.455
CV[%CP] 11.991 10.222 10.695 9.103 10.784 8.816 8.963 11.611
Min[x-fold] -6.989 -5.326 -5.679 -8.472 -6.134 -4.974 -5.399 -7.605
Max[x-fold] 895.323 125.453 153.711 19.862 213.149 129.505 198.218 1366.877
SD[+/- x-fold] 5.739 4.290 4.628 3.812 4.730 3.485 3.587 5.483
UBC YWHAZ
N 20.000 20.000
GM[CP] 20.542 20.417
AM[CP] 20.715 20.580
Min[CP] 18.000 18.000
Max[CP] 29.374 28.502
SD[+/- CP] 2.225 2.149
CV[%CP] 10.741 10.440
Min[x-fold] -5.823 -5.341
Max[x-fold] 455.742 271.510
SD[+/- x-fold] 4.675 4.434
$pair.Wise.cor
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP UBC YWHAZ
B2M 0.936 1.000 0.937 0.870 0.935 0.947 0.937 0.927 0.934 0.934
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
GAPD 0.979 0.937 1.000 0.959 0.996 0.970 0.975 0.971 0.986 0.985
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
HMBS 0.925 0.870 0.959 1.000 0.956 0.903 0.920 0.907 0.925 0.937
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
HPRT1 0.988 0.935 0.996 0.956 1.000 0.970 0.982 0.982 0.987 0.993
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
RPL13A 0.978 0.947 0.970 0.903 0.970 1.000 0.969 0.971 0.980 0.972
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
SDHA 0.987 0.937 0.975 0.920 0.982 0.969 1.000 0.988 0.991 0.987
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
TBP 0.994 0.927 0.971 0.907 0.982 0.971 0.988 1.000 0.986 0.991
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
UBC 0.987 0.934 0.986 0.925 0.987 0.980 0.991 0.986 1.000 0.986
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
YWHAZ 0.995 0.934 0.985 0.937 0.993 0.972 0.987 0.991 0.986 1.000
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
$HKG.vs.BestKeeper
ACTB B2M GAPD HMBS HPRT1 RPL13A SDHA TBP
coeff. of corr. [r] 0.994 0.951 0.993 0.945 0.996 0.983 0.990 0.989
coeff. of det. [r^2] 0.989 0.905 0.985 0.893 0.992 0.965 0.981 0.979
intercept [CP] -3.934 1.826 -0.318 3.959 -0.933 2.778 1.994 -3.861
slope [CP] 1.202 0.902 1.011 0.831 1.046 0.850 0.894 1.205
SE [CP] 0.361 0.822 0.348 0.805 0.268 0.451 0.349 0.498
p-value 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Power [x-fold] 2.301 1.869 2.015 1.779 2.065 1.803 1.859 2.305
UBC YWHAZ
coeff. of corr. [r] 0.993 0.995
coeff. of det. [r^2] 0.987 0.991
intercept [CP] -1.354 -0.616
slope [CP] 1.063 1.021
SE [CP] 0.348 0.277
p-value 0.000 0.000
Power [x-fold] 2.090 2.029
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