I''m new to R and deseq2 so apologies I'm made silly mistakes. I have three conditions with three replicates each. They are control, infection and attenuated infection. I have carried out analysis using 3 factor levels and used a contrast afterwards. I want to look at whats different between infection and attenuated infection (p.adjust<0.01, lfcThreshold=1), and take this output to make a heatmap including all conditions.
The contrast is:
res = results(dds, contrast=c("condition","infection ","attenuated infection"))
I can filter on p.ajust:
sig = which(cres$padj < 0.05)
I can't figure how to filter on logfoldchange after I used the contrast, I can do it before but then I can't use the contrast on the output from this.
resBigFC <- results(dds, lfcThreshold=1, altHypothesis="greaterAbs")