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-normalised???) data... is that correct? so what's the best package and working strategy?
If you plan to use limma / voom or DESeq2, then the best would be to obtain the raw counts and then follow the guidance for these programs.
You cannot, in any easy fashion, take FPKM expression units and re-process them using either of these programs.