Re: [GDAC-users] RSEM for STAD

Subject:   Re: [GDAC-users] RSEM for STAD (more for this subject)
From:   Hailei Zhang <> (more from this sender)
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 <> 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 <> wrote:
>
>> OK, thanks.
>>
>>
>> On Fri, Mar 28, 2014 at 10:52 AM, Hailei Zhang <
>> > 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 <>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
>>>>
>>>
>>>
>>
>
 
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