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:   Andrew Cherniack <hidden> (find more)
Date:   Oct 19, 2015 18:02

When I first looked at this page I ignored the mRNAseq column and
instinctively went to the mRNA column which is why I thought half of the
data was missing.
It took me about 3 minutes to figure out that all of the expression
profiles were available by clicking on the mRNAseg column.
The point is to people not familiar with TCGA who do not know that both
RNAseq and RNA Arrays have been run for certain projects the label RNA is
very confusing. It wouldn't be if you just added the word array after RNA.
 
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 2:33 PM, Michael Noble <hidden>
wrote:
 
> 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 <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
>>> <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
>>>
>>>
>>> <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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