Is they any R package to download processed miRNA expression levle from TCGA?

Question

[jack]

Hi all,

I would like to download processed miRNA expression levels for different cancers from TCGA. I was wondering whether is there any package such that I can use it to download data?

I tried to download manually from ICGC, but miRNAs are not annotated.

I was wondering whether can you help me with that?

Answer 1

[ivivek_ngs]

Yes there is one, have you tried TCGA2STAT. This should help you to get both count data or microarray intesities or even normalized expression (RPKM/FPKM) for cancer you are looking for. Just look up to the TCGA GDC portal to understand what data is first available for your desired cancer. When you say processed, I reckon it will be count data if its RNASeq and not normalized since you want to perform the statistical tests on them. However, I fear you will find more microarray intensity values on TCGA for miRNA rather than RNASeq.