I have FPKM-UQ data from COAD-TCGA.
I generated an expression set of this data using:
> edata = log2(data + 1)
> edata[1:2,1:2]
X01240896.3f3f.4bf9.9799.55c87bfacf36
1 8.540967
10 13.528968
100 16.296422
1000 13.658199
10000 15.143788
X01ad5016.f691.4bca.82a0.910429d8d25b
1 9.886537
10 16.719682
100 17.212312
1000 10.317842
10000 13.166767
Row name is entrezid, and column names are case_ids.
The batch data provided by TCGA which indicates a total batch num = 42
> omics[1:5,]
snf boo order batch
X01240896.3f3f.4bf9.9799.55c87bfacf36 3 192807 1 22
X01ad5016.f691.4bca.82a0.910429d8d25b 2 82213 2 2
X01f493d4.229d.47a6.baa8.32a342c65d01 1 A08907 3 29
X022f39e9.57ee.4b2b.8b3a.8929e3d69a37 2 A16S13 4 32
X02f9668c.71e6.485f.88b1.b37dc8bdd2ab 3 102113 5 7
> batch = omics$batch
> batch
[1] 22 2 29 32 7 1 8 8 7 41 26 14 26 26 1 5 22 5 15 18 28 12 12 8 19
[26] 13 38 5 27 7 41 1 22 26 28 22 33 14 13 8 10 13 11 17 5 38 5 7 7 31
[51] 22 42 11 8 7 17 15 17 12 17 2 19 2 12 18 14 22 11 21 15 17 17 33 15 19
[76] 15 6 1 10 11 2 28 36 17 9 15 12 17 15 10 6 8 13 25 11 15 1 13 24 8
[101] 13 15 17 8 2 22 17 11 13 37 19 38 13 19 5 16 5 5 22 35 35 19 13 17 22
[126] 7 8 8 41 39 14 6 19 18 38 22 14 30 19 24 11 14 13 16 7 13 8 22 12 8
[151] 22 17 2 40 13 35 15 5 24 19 41 22 22 19 17 8 13 33 10 17 29 12 9 11 24
[176] 27 5 14 7 25 13 35 9 18 16 13 31 25 18 10 35 18 14 33 5 19 17 8 11 11
[201] 42 7 10 8 39 19 8 7 11 19 31 35 28 36 13 37 10 38 3 18 13 34 39 13 3
[226] 40 31 17 19 26 7 19 12 22 19 17 12 17 13 12 28 33 37 17 35 18 40 13 20 35
[251] 17 6 15 14 12 27 5 41 31 41 18 21 19 17 40 8 41 2 5 15 5 15 15 5 39
[276] 1 22 33 13 17 7 11 15 3 7 38 15 7 14 14 22 31 14 18 3 19 7 9 6 5
[301] 22 8 11 1 13 10 19 8 14 15 6 32 1 2 19 4 5 13 18 42 11 17 8 36 19
[326] 15 22 28 15 8 11 8 15 38 19 39 7 11 42 23 5 1 22 17 35 13 40 25 7 41
[351] 38 5 8 19 31 6 38 8 36 4 15 15 7 12 22 38 29 35 15 2 10 2 19 15 25
[376] 5 39 30 19 18 15 10 10 33 1 19 32 19 19 15 20 15 7 22 35 22 30 14 12 16
[401] 21 13 15 18 7 5 6 31 12 7 15 32 33 18 14 15 15 26 31 1 14 19 17 18 1
[426] 5 10 32
Unfortunately, when I run the ComBat analysis it generates all NANs, and no values:
> modcombat = model.matrix(~1, data=omics)
> combat_edata = ComBat(dat=edata, batch=batch, mod=modcombat, par.prior=TRUE, prior.plots=FALSE)
> combat_edata[1:5,1:2]
X01240896.3f3f.4bf9.9799.55c87bfacf36
1 NaN
10 NaN
100 NaN
1000 NaN
10000 NaN
X01ad5016.f691.4bca.82a0.910429d8d25b
1 NaN
10 NaN
100 NaN
1000 NaN
10000 NaN