FPKM, FPKM-UQ, TPM or counts: How do I know which kind of unit should I use? 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
Type of data you need depends on the downstream applications and since you would like to carry out DEA with DESeq2, you would need raw counts (non-normalized).
There are many ways to import/download TCGA data, one such tool, the TCGAbiolinks package gives a nice interface for not only downloading the read count (or pre-processed) data but also associated clinical data.