Raw counts TCGA Firebrowse

Question

[Folder40g]

Hi

I've downloaded some data from firebrowse. I know some data is in RSEM format. But my question is. Why a file such SKCM.uncv2.mRNAseq_raw_counts.txt, which in theory is just the raw counts it contains decimals?

I would expect decimals in normalized and RSEM but not in the raw data. Just want to perform some differential expression analysisis between two cohorts.

So if I'm not wrong this file is jsut the raw counts transformed into RSEM. But whats the difference between this file and the SKCM.uncv2.mRNAseq_RSEM_all.txt ?

Thanks

Answer 1

[Kevin Blighe]

Great question. I am almost certain that the answer lies in the fact that it's RNA-seq v2 data, s to which you have already implied. I also believe that it's an unfortunate naming of the file by the Broad in calling it 'raw'. I think that the 'raw' counts are the RSEM estimate counts (thus, decimals), whereas the other file contains the RSEM estimate counts that have been normalised by tags/transcripts per million

You may want to seek clarification from the Broad.