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 13:22

You can also check the data set in the TCGA website.
https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp
 
Best,
Hailei
 
On Tue, Oct 21, 2014 at 1:19 PM, Fabrice Sircoulomb <hidden>
wrote:
 
> 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 13:11, Hailei Zhang <hidden> wrote:
>
> 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 5 of 15)

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

    Hi Fabrice, This is not the common case. The mRNAseq was processed by UNC. I think they did not finish processing old samples yet

    • 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 ...

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

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

          Hi Hailei, I have one more question about the RNAseq data. You mentioned that the RNAseqV1 and RNAseqV2 were generated using 2 different pipelines. But is the data coming from the same experiment? Regards, Fab (5 more messages in this thread)

      • Re: [GDAC-users] mRNAseq expression data TCGA Michael Noble <hidden>

        You could also access them programmatically from the API: http://firebrowse.org/apidocs/#!/Samples/mRNASeq