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

Subject:   Re: [GDAC-users] TCGA GDAC breast caner methylation analysis help (find more)
From:   Michael Noble <hidden> (find more)
Date:   Oct 24, 2015 09:40

Lastly, David:  since spring of 2014 these preprocessed data have been available in the stddata packages.  You can retrieve them in the FireBrowse ui (for example, see below) or with firehose_get or the FireBrowse archives API or the fbget Python/Unix client tool.
 
Best,
Mike
 
 
On Oct 23, 2015, at 8:07 PM, Michael Noble <hidden> wrote:
 
> I’ve posted the file to
>  
>  http://gdac.broadinstitute.org/runs/tmp/methylated_genes_brca__2012_08_25/BRCA.meth.for_clustering.filtered_data.txt.gz
>  
> Take note that, even compressed, it’s 37 MB.  I hope this helps.
>  
> Regards,
> -Mike
>  
>  
> On Oct 23, 2015, at 7:32 PM, Michael Noble <hidden> wrote:
>  
>> 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.
>>  
>> Best,
>> -Mike
>> —
>>  
>> 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 <hidden> wrote:
>>  
>>> Hi,
>>>  
>>> I was trying to access the gene list for the 8586 highly variable methylation genes from the analysis on this site:
>>>  
>>> http://gdac.broadinstitute.org/runs/analyses__2012_08_25/reports/cancer/BRCA/methylation/clustering_CNMF/nozzle.html
>>>  
>>> 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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PNG File meth-data-prepr.png (452 kB - Anonymous - Oct 24, 2015)
Entire Thread (Showing 3 of 4)

  • Re: [GDAC-users] TCGA GDAC breast caner methylation analysis help Michael Noble <hidden>

    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