NaN values after ComBat analysis on TCGA COAD RNAseq
I think I might know what the problem is. 

I plotted the log2 corrected values, and the distribution may not be normal because of the 0 values present in RNASeq data. If I understand correctly, this data is actually missing, whereas with my current analysis it is viewed by R as an actual value of 0. So either the missing data needs to be imputed, or the data needs to be scaled and normalized to mean of 0, then subsequently log2 transformed.

&gt; data &lt;- standardNormalization(data)
&gt; data &lt;- log2(data + 1)
&gt; combat_data = ComBat(dat=data, batch=batch, mod=modcombat, par.prior=TRUE, prior.plots=FALSE)
&gt; combat_data[1:5,1:2]
          X01240896.3f3f.4bf9.9799.55c87bfacf36
100507661                           -0.13857428
57103                               -0.06700506
22838                                0.16295096
55567                               -0.13579991
6147                                 1.64990772
          X01ad5016.f691.4bca.82a0.910429d8d25b
100507661                           -0.13789534
57103                               -0.06210232
22838                                0.01546224
55567                               -0.13443289
6147                                 1.48473072