This is not the common case. The mRNAseq was processed by UNC. I think they
did not finish processing old samples yet.
On Tue, Oct 21, 2014 at 12:26 PM, Fabrice Sircoulomb <hidden>
> But when I look at the data from the firehose (
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
> 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.
> 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?
>> 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.
>> On Mon, Oct 20, 2014 at 5:25 PM, Fabrice Sircoulomb <
>> hidden> wrote:
>>> 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
>>> I saw that there is 2 versions of mRNAseq expression data (RNAseqV1 and
>>> 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?
>>> 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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