Hi,
I am comparing 2 conditions ; I would like to find all genes that show less than a 2fold increase in condition A vs B, wether the fold change is positive or negative. (and reciprocally genes that show not a 2fold decrease). Is that possible?
I tried results(dds, lfcThreshold=1, altHypothesis="less") and select padj<0.01, but in fact that select the genes for which lfc(A/B) < -1 is significant, whereas I would like lfc(A/B) < 1 is significant (that is altHypothesis="less" and altHypothesis="lessAbs").
Does the 1-pValue of results(dds, lfcThreshold=1, altHypothesis="greater") would give me the pValue I am looking for? (sorry if this is a statistical nonsense, I cannot judge myself).