Re: [GDAC-users] mRNAseq expression data TCGA

Subject:   Re: [GDAC-users] mRNAseq expression data TCGA (find more)
From:   Hailei Zhang <hidden> (find more)
Date:   Oct 21, 2014 13:11

Hi Fabrice,
 
This is not the common case. The mRNAseq was processed by UNC. I think they
did not finish processing old samples yet.
 
Best,
Hailei
 
On Tue, Oct 21, 2014 at 12:26 PM, Fabrice Sircoulomb <hidden>
wrote:
 
> But when I look at the data from the firehose (
> http://firebrowse.org/?cohort=OV) I found more sample with RNAseqV1.
> I have 265 samples with RNAseqV2 and 299 samples with RNAseqV1 (the
> intersection between RNAseqV1 and V2 is 264).
> Is it normal?
> Thank you very much
> Fab
>
> On 21 Oct 2014, at 10:37, Hailei Zhang <hidden> wrote:
>
> The RNAseq v1 was processed by the old analysis pipeline which is not used
> any more after the new analysis pipeline was launched.
>
> All the old samples were also analyzed by v2 pipeline. This is why you
> will see that there will be more samples in RNAseq v2.
>
> Best,
> Hailei
>
> On Tue, Oct 21, 2014 at 10:22 AM, Fabrice Sircoulomb <
> hidden> wrote:
>
>> Thank you.
>> Could you comment why is there a different number of sample with RNAseqV1
>> and RNAseqV2?
>> Best,
>> Fabrice
>>
>> On 20 Oct 2014, at 22:14, Hailei Zhang <hidden> wrote:
>>
>> Hi Fabrice,
>>
>> You are right. The RNAseq V2 is the RSEM values which is better than the
>> v1 RPKM values.
>>
>> Best,
>> Hailei
>>
>> On Mon, Oct 20, 2014 at 5:25 PM, Fabrice Sircoulomb <
>> hidden> wrote:
>>
>>> Hi,
>>>
>>> I am planning to use the gene expression data from the TCGA. More
>>> precisely, I want to compare the expression of one gene between 2 groups of
>>> samples.
>>> I saw that there is 2 versions of mRNAseq expression data (RNAseqV1 and
>>> RNAseqV2).
>>> From my understanding RNAseqV2 expression data was derived using RSEM
>>> which is better at estimating gene/transcript abundance.
>>> Could you confirm?
>>> If yes, I would think it is better for me to use the RNAseqV2 version.
>>> Am I correct?
>>>
>>> Thanks
>>> Best,
>>>
>>>
>>> Fabrice Sircoulomb
>>> Post-doctoral Fellow
>>> Dr Rottapel Lab
>>> Toronto Medical Discovery Tower
>>> MaRS East Tower, 101 College Street
>>> Rm 12-701, Toronto, ON M5G 1L7 CANADA
>>> phone: 416-581-7855
>>>
>>>
>>
>>
>
>
 
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Entire Thread (Showing 4 of 15)

  • Re: [GDAC-users] mRNAseq expression data TCGA Hailei Zhang <hidden>

    RNAseq v1 was processed by the old analysis pipeline which is not used any more after the new analysis pipeline was launched

    • Re: [GDAC-users] mRNAseq expression data TCGA Fabrice Sircoulomb <hidden>

      when I look at the data from the firehose (http://firebrowse.org/?cohort=OV) I found more sample with RNAseqV1. I have 265 samples with RNAseqV2 and 299 samples with RNAseqV1 (the intersection between RNAseqV1 and V2 is 264). Is it normal? Thank ...

      • Re: [GDAC-users] mRNAseq expression data TCGA Hailei Zhang <hidden>

        • Re: [GDAC-users] mRNAseq expression data TCGA Fabrice Sircoulomb <hidden>

          Just for my reference, where should I look/check for the updated mRNAseq data? Is that address http://firebrowse.org/?cohort=OV the one? Any other place? Thanks for your help Hailei. Best, Fab On 21 Oct 2014, at 13 ... (8 more messages in this thread)