pairwise.mod.t.test: Pairwise Moderated t-Tests
In MKomics: Omics Data Analysis

Description Usage Arguments Details Value References See Also Examples

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 `p.adjust`
`sort.by`	see `toptable`

, 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.

oneway.test, mod.t.test

set.seed(123)
X <- rbind(matrix(rnorm(5*20), nrow = 5, ncol = 20),
           matrix(rnorm(5*20, mean = 1), nrow = 5, ncol = 20))
gr <- factor(c(rep("A1", 5), rep("B2", 5), rep("C3", 5), rep("D4", 5)))
mod.oneway.test(X, gr)
pairwise.mod.t.test(X, gr)

topTableF is obsolete and will be removed in a future version of limma.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