[GDAC-users] Re: Number of cases missing for mRNAseq in BRCA

Subject:   [GDAC-users] Re: Number of cases missing for mRNAseq in BRCA (find more)
From:   Andrew Cherniack <hidden> (find more)
Date:   Oct 19, 2015 10:17

Yes I understand that but having the label RNA is very ambiguous to
scientists looking at the data.
You make the distinction between low pass and SNP 6.0 copy number.
I would suggest that you change the label RNA to RNA - microarray to make
it more clear and easier to understand.
 
Andy
 
___________________________
Andrew Cherniack, PhD
Group Leader
Cancer Program
Broad Institute of Harvard and MIT
415 Main Street
Cambridge, Mass 02142
email: hidden
___________________________
 
On Mon, Oct 19, 2015 at 10:13 AM, Michael Noble <hidden>
wrote:
 
> Good Morning Andy,
>
> We do label them distinctly:
>
> mRNASeq is labeled to clearly indicate that it is sequence-based
> mRNA is not
>
> That these are processed differently and represent different data types
> (array-based, versus sew-based) is also described in our online
> documentation
> <https://confluence.broadinstitute.org/display/GDAC/Documentation#Documentation-ExpressionMicroarrayprocessing>.
> And that documentation page
> <https://confluence.broadinstitute.org/display/GDAC/Documentation> is visible
> directly from our top-level home page <http://gdac.broadinstitute.org/> (as
> shown below).
>
> Hope this helps,
> Mike
>
>
>
>
> On Oct 19, 2015, at 9:58 AM, Andrew Cherniack <hidden>
> wrote:
>
> Never mind I just figured it out.
> You guys should label mRNA  - mRNA microarray to keep it distinguished
> from RNAseq.
>
> Andy
>
> ___________________________
> Andrew Cherniack, PhD
> Group Leader
> Cancer Program
> Broad Institute of Harvard and MIT
> 415 Main Street
> Cambridge, Mass 02142
> email: hidden
> ___________________________
>
> On Mon, Oct 19, 2015 at 9:56 AM, Andrew Cherniack <
> hidden> wrote:
>
>> Why are half of the RNA seq cases missing in FireBrowse for BRCA.
>> I am working with the BRCA group and I know that ~1000 cases have been
>> profiled.
>>
>> Andy
>>
>
>
>
 
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