[BioC] questions on edgeR package

Steve Lianoglou 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.


Steve Lianoglou
Computational Biologist

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