I'm getting inconsistent numbers of genes from DESeq2 results.
Using the default FDR, On summary(res), I have:
out of 26572 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 2117, 8% LFC < 0 (down) : 1675, 6.3% (i.e., total `3792`)
However, if I subset using either of the following, I get 2 less genes (
resSig <- res[which(res$padj<0.1),] resSig <- subset(res, res$padj<0.1)
This really doesn't make any sense at all! Any thoughts?
I also get a different value for padj<0.05 if I subset the above results table or if I run DESeq with alpha=0.05, thoughthat is answered by Michael Love here: http://seqanswers.com/forums/archive/index.php/t-41887.html