Re: [GDAC-users] RSEM for STAD

Subject:   Re: [GDAC-users] RSEM for STAD (find more)
From:   Hailei Zhang <hidden> (find more)
Date:   Mar 28, 2014 13:42

Hi Mike,
 
Here is the paper about RSEM: http://www.biomedcentral.com/1471-2105/12/323.
It is different from RPKM.
 
Best,
Hailei
 
 
On Fri, Mar 28, 2014 at 11:50 AM, Michael Rooney <hidden> wrote:
 
> Followup question:
>
> When I look at the normalized gene-level RSEM values on firehose, the
> expression (across all genes) adds up to somewhere between 17,000,000 and
> 23,000,000 for each sample. However, I thought that that RSEM was designed
> so that abundances add to 1 (or to 1 million, if you desire TPM). So how do
> I interpret this?
>
> Thanks,
> Mike
>
>
> On Fri, Mar 28, 2014 at 10:56 AM, Michael Rooney <hidden> wrote:
>
>> OK, thanks.
>>
>>
>> On Fri, Mar 28, 2014 at 10:52 AM, Hailei Zhang <hidden
>> > wrote:
>>
>>> Hi Mike,
>>>
>>> The mRNAseq of STAD was processed by bcgsc not by UNC. The bcgsc only
>>> provide the RPKM value.
>>>
>>> Best,
>>> Hailei
>>>
>>>
>>> On Thu, Mar 27, 2014 at 12:51 PM, Michael Rooney <hidden>wrote:
>>>
>>>> Hi,
>>>>
>>>> When I look on firehose, I do not see RSEM expression estimates for
>>>> STAD. Is there a reason for this? Am I mistaken?
>>>>
>>>> Thanks,
>>>> Mike
>>>>
>>>
>>>
>>
>
 
To unsubscribe from this group and stop receiving emails from it, send an email to hidden.
Entire Thread (Showing 4 of 6)

  • Re: [GDAC-users] RSEM for STAD Michael Rooney <hidden>

    OK, thanks. On Fri, Mar 28, 2014 at 10:52 AM, Hailei Zhang <hailei@broadinstitute.org>wrote

    • Re: [GDAC-users] RSEM for STAD Michael Rooney <hidden>

      Followup question: When I look at the normalized genelevel RSEM values on firehose, the expression (across all genes) adds up to somewhere between 17,000,000 and 23,000,000 for each sample. However, I thought that that RSEM was designed so that abundances add ...

      • Re: [GDAC-users] RSEM for STAD Hailei Zhang <hidden>

        • Re: [GDAC-users] RSEM for STAD Michael Rooney <hidden>

          Thanks. I am aware that RSEM is different from RPKM. It is my understanding that RSEM estimates are supposed to sum to 1. Ppl. on the Broad 6th floor say that this is the case. So I am confused by why the numbers in the firehose expression files ...