# 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.
• limma was designed for microarray data, but can be used for RNA-seq by using the voom transformation. However, the gold standard these days is DESeq2. As for how many datasets you need... what's your hypothesis? What are you looking for? Do you just want to blindly do tumor vs normal for multiple cancer types and check what comes up? Sep 4 '20 at 9:44