I downloaded the raw data from the current GTEX release (http://www.gtexportal.org/home/). I parsed the data to get a matrix of a couple of genes and their associated RPKM values in a bunch of different samples. E.g. I have 6 samples isolated from the cervix, 10 samples isolated from skin, 25 samples from vagina.
I am interested in calculating the differential expression of these genes in these tissues.
Since RPKM are not raw counts, I will not be able to use most standard pipelines to calculate differential expression. Could anyone recommend a tool that I could use? Does anyone have experience with DEGSeq?
Also, how do I combine samples? Can I just consider them to be replicates?
As always, thanks...