Hello,

I'm working on some RNAseq data from The Cancer Genome Atlas, and the relevant gene expression data is given in Fragments Per Kilobase of transcript per Million mapped reads (FPKM). I'm looking to run a differential gene expression analysis on this data, for specific genes between specific sets of samples, but am unsure of the best possible package and method to do this.

Thanks.

Check out Gordon's answer to a related question (A: Differential expression of RNA-seq data using limma and voom()). Long story short, the best solution is to try to get the original count data; check out the response in this post (A: Can I feed TCGA normalized count data to EdgeR for differential gene expression ) where they've collated TCGA count data with Rsubread for this express purpose.