I'm trying to download data from the TCGA for gene expression analyses in R, but I'm in doubt if I should use FPKM, FPKM-UQ or counts? When the dataset is in counts, I suppose it's raw data, isn't it? So what's the best unit to compare multiple datasets?
I'm planning to use limma or Dseq2 for GE analysis and found that with Dseq2 I need to use count(non-normalized???) data... is that correct? so what's the best package and working strategy?
thank you very much, Fabiano