I am running a rna seq differential gene expression experiment with the following code:
dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,design =~Age+Gender+Response) dds <- DESeq(dds) res <- results(dds,contrast=c("Response","Yes","No"))
Looking at the results I get about thousands genes with absolute log fold change > 0.5.
However, when I run the following command:
resGA <- results(dds, lfcThreshold=0.5, altHypothesis="greaterAbs")
I only get 256 with absolute log fold change > 0.5.
Anyone can help me figure out what is the source of this discrepancy?