I have a expression profile (RNAseq) of 580 immune-related genes for 350 samples that are already classified into 4 subtypes. I want to find the genes (out 0f 580) that significantly have different expression among these 4 subtypes. In an article Significance analysis of microarrays (SAM) method was used to identify differential expression gene between multiple groups. However my data is RNAseq and I couldn't figure out how to use SAM for my data?
Is there any other ways or packages in r that can do this?
Really appreciate any suggestion!