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 10:37

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>

    Hi Fabrice, You are right. The RNAseq V2 is the RSEM values which is better than the v1 RPKM values

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

      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 <hailei@broadinstitute.org> wrote

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

        • 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 ... (10 more messages in this thread)