Re: [GDAC-users] TCGA GDAC breast caner methylation analysis help

Subject:   Re: [GDAC-users] TCGA GDAC breast caner methylation analysis help (more for this subject)
From:   Michael Noble <> (more from this sender)
Date:   Oct 23, 2015 19:32

Hello David,
Yes, you are correct:  the output of the preprocessor that is used internal to identify the most highly methylated genes is not packaged.   We will correct that oversight soon.  In the meantime, we’ll dig up that input file and send it along to you directly.

Michael S. Noble
Assistant Director for Data Science
Cancer Genome Computational Analysis
The Broad Institute of MIT & Harvard
Manager, Genome Data Analysis Center
The Cancer Genome Atlas
On Oct 23, 2015, at 11:55 AM, Frankhouser, David <> wrote:
> Hi,
> I was trying to access the gene list for the 8586 highly variable methylation genes from the analysis on this site:
> I have downloaded all available data, and I am unable to get a list of genes (or even probe ids) for those 8586 genes. The closest that I could come is to use the marker genes reported in Table 3 which contains ~8300 unique genes.  
> One issue is that the under the "Download results" section, the MAGE-TAB link results in a 404 error and can not be downloaded.
> If you could help me out in identifying the 8586 genes, that would be very appreciated.
> Thank you in advance for you time and help!
> Cheers,
> David Frankhouser
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