Differential Expression Analysis Using RPKM

Question

[bryan.yankee27]

I am a student researcher studying the gene expression of a virulent manifestation of a disease compared to non-severe cases of that same disease. I have tables containing the RPKM values for 8 samples (4 control and 4 treatment) containing ~3000 genes. How would you recommend going about differential expression analysis? I am hoping to generate P-values and then take the log2 transformations of the RPKM values to generate a volcano plot for this data. Are there any programs or methods that you are aware of that would enable me to do DE analysis using only the RPKM values for these 8 samples?

Answer 1

[swbarnes2]

Limma might work.