Re: [GDAC-users] mRNAseq expression data TCGA

Subject:   Re: [GDAC-users] mRNAseq expression data TCGA (more for this subject)
From:   Hailei Zhang <> (more from this sender)
Date:   Oct 27, 2014 15:40

Hi Fab,
 
The overlapped samples are from the same experiments. Only the analysis
pipeline was changed. The bam files were not changed.
 
Best,
Hailei
 
 
On Mon, Oct 27, 2014 at 3:33 PM, Fabrice Sircoulomb <>
wrote:
 
> 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
>
> On 21 Oct 2014, at 13:22, Hailei Zhang <> wrote:
>
> 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 <
> > 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 <> 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 <
>> > 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 <>
>>> 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 <
>>> > 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 <>
>>>> 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 <
>>>> > 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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