Question

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

0

Entering edit mode

5.8 years ago

jack ▴ 960

Hi all,

I would like to download processed miRNA expression levels for different cancers from TCGA. I was wondering whether is there any pakage such that I can use it to download data ? I tried to dowload maually from ICGC, but miRNAs are not annotated. I was wondering whether can you help me with that ?

RNA-Seq next-gen tca bioinformatics • 1.7k views

ADD COMMENT • link updated 5.8 years ago by ivivek_ngs ★ 5.2k • written 5.8 years ago by jack ▴ 960

score 2 · Answer 1 · 2017-05-03

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.