[BioC] questions on edgeR package

[Gordon K Smyth]

On Wed, 29 Jan 2014, Steve Lianoglou wrote:

> 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.

I think the point is that Ming has already downloaded the v2 data, and the 
so-called "raw counts" turned out not to be counts.

If you want to dig to find out what the "raw counts" are exactly, that 
would be a great service, because I am just guessing.  The TCGA 
documentation just says they are from RSEM.

Gordon


> HTH,
> -steve
>
> -- 
> Steve Lianoglou
> Computational Biologist
> Genentech

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