I'm interested in testing which genes are not significantly downregulated. While I'm able to get genes significantly upregulated with the following code:
resUp <- results(dds, lfcThreshold=0, altHypothesis="greater")
And genes significantly unregulated with the following code:
resLA <- results(dds, lfcThreshold=1, altHypothesis="lessAbs")
I'm unable to define genes significantly NOT downregulated using altHypothesis = "greater" and lfcThreshold = -1 as the lfcThreshold must be a non-negative value. Is there another way to directly test this?