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

Subject:   Re: [GDAC-users] Number of cases missing for mRNAseq in BRCA (find more)
From:   Michael Noble <hidden> (find more)
Date:   Oct 19, 2015 14:33

But 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 red bar labeled as 1093 mRNASeq samples …which seems very clear to me .. so, is is there somewhere else in the software stack that you’re referring to, Andy?
 
Thanks,
Mike
 
 
   
 
 
On Oct 19, 2015, at 11:42 AM, Gad Getz <hidden> wrote:
 
> I agree that mRNAseq and mRNAarray would be much clearer.
>  
> Thanks,
>      Gaddy
>  
> ---------
> For administrative assistance please contact Lidia Graziano
> (hidden  or 617-714-7390)
>  
> 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.  And that documentation page is visible directly from our top-level home page (as shown below).
>  
> Hope this helps,
> Mike
>  
>  
>   <Screen Shot 2015-10-19 at 10.11.44 AM.png>
>  
>  
> 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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PNG File Screen Shot 2015-10-19 at 2.21.17 PM.png (81 kB - Anonymous - Oct 19, 2015)
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