[BioC] questions on edgeR package
lianoglou.steve at gene.com
Thu Jan 30 03:03:54 CET 2014
On Wed, Jan 29, 2014 at 4:52 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
> I have checked with my lab, and I was incorrect to say that we have
> downloaded SRA files for TCGA -- it was actually downloaded RSEM counts that
> we downloaded. I think it would be a good idea for people like you to put
> pressure on TCGA to make unprocessed data available.
I am not an expert on accessing TCGA data, but:
The raw data is available, but restricted due to
privacy/confidentiality concerns for patients. One could get access to
the truly raw data via an application:
Also, the following page suggests that some type of "raw expression"
("raw counts" and RPKM) should be accessible from their RNASeq v2
So, perhaps tha v2 data might be helpful there.
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