Description Usage Arguments Details Value References See Also Examples
View source: R/pairwise.mod.t.test.R
Performs pairwise moderated t-tests (unpaired) based on Bioconductor package limma.
1 | pairwise.mod.t.test(x, group, adjust.method = "BH", sort.by = "none")
|
x |
a (non-empty) numeric matrix of data values. |
group |
an optional factor representing the groups. |
adjust.method |
see |
sort.by |
see |
, where "logFC"
corresponds to difference in means.
The function uses Bioconductor package limma to compute pairwise moderated
t-tests. For more details we refer to ebayes
.
A data.frame with the results.
Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47.
1 2 3 4 5 6 |
topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
A1 vs B2 A1 vs C3 A1 vs D4 B2 vs C3 B2 vs D4 C3 vs D4
1 1.0974330 0.2271669 0.26827976 -0.87026609 -0.8291532 0.04111286
2 0.0769194 0.9622020 -0.61252965 0.88528264 -0.6894491 -1.57473169
3 -0.3105477 -0.7130963 -0.58266984 -0.40254866 -0.2721221 0.13042651
4 -0.5832304 -0.2440290 -0.03386782 0.33920142 0.5493626 0.21016117
5 -0.9579128 -0.4501003 -0.61874146 0.50781250 0.3391713 -0.16864116
6 -0.6013595 -0.5109767 -0.15342834 0.09038278 0.4479311 0.35754833
7 0.3471695 -0.3493145 -0.68975433 -0.69648400 -1.0369239 -0.34043986
8 -0.9277388 -0.5691081 -0.71053196 0.35863064 0.2172068 -0.14142382
9 -0.5998638 -1.5488157 -0.14153255 -0.94895185 0.4583313 1.40728311
10 1.5527067 0.5179562 0.99934740 -1.03475050 -0.5533593 0.48139118
grand mean F p.value adj.p.value
1 0.22133220 1.4119467 0.23709800 0.5868380
2 0.06743767 2.5678204 0.05255479 0.1751826
3 -0.05806215 0.6094415 0.60879068 0.7253749
4 0.10864239 0.4386138 0.72537489 0.7253749
5 0.11267943 0.9691456 0.40611786 0.5868380
6 1.13404486 0.5002131 0.68212276 0.7253749
7 1.02060384 1.2185746 0.30111975 0.5868380
8 0.61908872 0.9594030 0.41078662 0.5868380
9 1.19472748 2.9871234 0.02980893 0.1751826
10 0.49380111 2.6903326 0.04456696 0.1751826
A1-B2 A1-B2: t A1-B2: p A1-B2: adj.p A1-B2: B A1-C3
1 1.0974330 1.9176595 0.056935659 0.26739434 -4.150296 0.2271669
2 0.0769194 0.1344093 0.893247840 0.89324784 -5.826707 0.9622020
3 -0.3105477 -0.5426525 0.588124185 0.65347132 -5.700081 -0.7130963
4 -0.5832304 -1.0191395 0.309675276 0.44239325 -5.359162 -0.2440290
5 -0.9579128 -1.6738612 0.096111665 0.26739434 -4.551426 -0.4501003
6 -0.6013595 -1.0508183 0.294926580 0.44239325 -5.329122 -0.5109767
7 0.3471695 0.6066456 0.544945915 0.65347132 -5.666387 -0.3493145
8 -0.9277388 -1.6211350 0.106957735 0.26739434 -4.631016 -0.5691081
9 -0.5998638 -1.0482048 0.296125067 0.44239325 -5.331635 -1.5488157
10 1.5527067 2.7132069 0.007393498 0.07393498 -2.462559 0.5179562
A1-C3: t A1-C3: p A1-C3: adj.p A1-C3: B A1-D4 A1-D4: t
1 0.3969525 0.691931480 0.69193148 -5.757494 0.26827976 0.46879329
2 1.6813563 0.094644661 0.47322331 -4.535810 -0.61252965 -1.07033714
3 -1.2460679 0.214560903 0.61819096 -5.119000 -0.58266984 -1.01815997
4 -0.4264174 0.670376894 0.69193148 -5.746391 -0.03386782 -0.05918078
5 -0.7865073 0.432733671 0.61819096 -5.546500 -0.61874146 -1.08119168
6 -0.8928830 0.373260796 0.61819096 -5.464740 -0.15342834 -0.26810139
7 -0.6103937 0.542467061 0.67808383 -5.659092 -0.68975433 -1.20527990
8 -0.9944622 0.321499481 0.61819096 -5.376999 -0.71053196 -1.24158683
9 -2.7064076 0.007539705 0.07539705 -2.477381 -0.14153255 -0.24731463
10 0.9050791 0.366784330 0.61819096 -5.454705 0.99934740 1.74626427
A1-D4: p A1-D4: adj.p A1-D4: B B2-C3 B2-C3: t B2-C3: p
1 0.63985549 0.8944242 -4.606903 -0.87026609 -1.5207070 0.13030713
2 0.28607955 0.5168984 -4.593186 0.88528264 1.5469470 0.12385169
3 0.31013903 0.5168984 -4.594801 -0.40254866 -0.7034154 0.48281925
4 0.95288197 0.9528820 -4.610107 0.33920142 0.5927221 0.55420392
5 0.28123878 0.5168984 -4.592840 0.50781250 0.8873539 0.37622030
6 0.78896661 0.8944242 -4.609094 0.09038278 0.1579353 0.87470693
7 0.22987482 0.5168984 -4.588637 -0.69648400 -1.2170394 0.22538132
8 0.21620608 0.5168984 -4.587321 0.35863064 0.6266728 0.53176683
9 0.80498180 0.8944242 -4.609252 -0.94895185 -1.6582029 0.09923575
10 0.08268426 0.5168984 -4.564982 -1.03475050 -1.8081278 0.07246459
B2-C3: adj.p B2-C3: B B2-D4 B2-D4: t B2-D4: p B2-D4: adj.p
1 0.3257678 -4.575899 -0.8291532 -1.4488662 0.14933196 0.6213576
2 0.3257678 -4.574706 -0.6894491 -1.2047465 0.23008017 0.6213576
3 0.6157821 -4.602828 -0.2721221 -0.4755075 0.63507382 0.7047841
4 0.6157821 -4.604954 0.5493626 0.9599587 0.33852439 0.6213576
5 0.6157821 -4.598493 0.3391713 0.5926696 0.55423902 0.6927988
6 0.8747069 -4.609789 0.4479311 0.7827169 0.43495030 0.6213576
7 0.4507626 -4.588215 -1.0369239 -1.8119255 0.07187282 0.6213576
8 0.6157821 -4.604340 0.2172068 0.3795482 0.70478410 0.7047841
9 0.3257678 -4.569423 0.4583313 0.8008902 0.42438292 0.6213576
10 0.3257678 -4.561724 -0.5533593 -0.9669426 0.33503202 0.6213576
B2-D4: B C3-D4 C3-D4: t C3-D4: p C3-D4: adj.p C3-D4: B
1 -4.579059 0.04111286 0.0718408 0.942818328 0.94281833 -5.862037
2 -4.588656 -1.57473169 -2.7516934 0.006613244 0.06613244 -2.377508
3 -4.606809 0.13042651 0.2279079 0.820008840 0.91112093 -5.840494
4 -4.596506 0.21016117 0.3672366 0.713927813 0.91112093 -5.802308
5 -4.604955 -0.16864116 -0.2946843 0.768617018 0.91112093 -5.824423
6 -4.601082 0.35754833 0.6247816 0.533004365 0.91112093 -5.684652
7 -4.561521 -0.34043986 -0.5948862 0.552759917 0.91112093 -5.701444
8 -4.608024 -0.14142382 -0.2471246 0.805128573 0.91112093 -5.836290
9 -4.600656 1.40728311 2.4590930 0.014993757 0.07496878 -3.079639
10 -4.596307 0.48139118 0.8411852 0.401499618 0.91112093 -5.538559
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