I was curious to fish out genes that are unaffected no-matter what was the condition. I am comparing GE in two tissues and I was hoping to find some genes whose expression doesn't vary.
For such genes, which do not show changes at genic level, I wish to see if there are changes at the isoform level or not.
Having said that I was using the following code to subset the genes (considering genes with FC<1.5 as unaffected genes)
subset(res, padj<=0.05 & abs(l$log2FoldChange)<0.58)
However, I don't get any genes at these cutoffs