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

Subject:   Re: [GDAC-users] Re: Number of cases missing for mRNAseq in BRCA (find more)
From:   Gad Getz <hidden> (find more)
Date:   Oct 19, 2015 11:42

I agree that mRNAseq and mRNAarray would be much clearer.
 
Thanks,
     Gaddy
 
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On Mon, Oct 19, 2015 at 10:17 AM, Andrew Cherniack <
hidden> wrote:
 
> 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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Entire Thread (Showing 4 of 8)

  • [GDAC-users] Re: Number of cases missing for mRNAseq in BRCA Michael Noble <hidden>

    Good Morning Andy, We do label them distinctly: mRNASeq is labeled to clearly indicate that it is sequencebased mRNA

    • [GDAC-users] Re: Number of cases missing for mRNAseq in BRCA Andrew Cherniack <hidden>

      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 ...

      • Re: [GDAC-users] Re: Number of cases missing for mRNAseq in BRCA Gad Getz <hidden>

        • Re: [GDAC-users] Number of cases missing for mRNAseq in BRCA Michael Noble <hidden>

          I don’t understand: this thread of discussion began by saying that we’re missing almost half of the mRNASeq samples from FireBROWSE … but if you visit http://firebrowse.org/?cohort=brca one instantly sees the graphic below, which has a brick ... (1 more message in this thread)