[BioC] questions on edgeR package

[Steve Lianoglou]

Hi,

On Wed, Jan 29, 2014 at 4:52 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
[snip]
> 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:

https://cghub.ucsc.edu/access/get_access.html

Also, the following page suggests that some type of "raw expression"
("raw counts" and RPKM) should be accessible from their RNASeq v2
pipeline):

https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2

So, perhaps tha v2 data might be helpful there.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech