Re: [GDAC-users] RSEM for STAD

Subject:   Re: [GDAC-users] RSEM for STAD (more for this subject)
From:   Michael Rooney <> (more from this sender)
Date:   Mar 28, 2014 18:25

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 do not follow this rule.
 
Thanks again,
Mike
 
 
On Fri, Mar 28, 2014 at 1:42 PM, Hailei Zhang <>wrote:
 
> 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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