I'd like to perform differential expression analysis with some RNA-seq samples from GEO database (GSE99987) and obtain significant genes between different conditions. However, the count tables that are available on GEO show FPKM normalized counts. This normalization was done by Cuffdiff (v2.2.1) as it is mentioned by the authors.
So my question is: Should I use FPKM-normalized counts for differential expression analysis without applying any other normalization (such as TMM, DESeq size factor...) ??
P.D: I am confused because I've always read that FPKM normalization was for comparison of gene counts within the same sample. Whereas TMM, DESeq... normalizations were for comparison of gene counts between different conditions (samples).
Thank you in advance, Goren