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:   Nov 26, 2014 10:57

Hi Fab,
 
We only process the level 3 data. The segment data was provided by other
group. Gordon may answer your question.
 
Best,
Hailei
 
On Tue, Nov 25, 2014 at 8:21 PM, Fabrice Sircoulomb <>
wrote:
 
> Hi Hailei,
>
> I have a question regarding the illumina Duo SNP copy number for the
> ovarian cohort. I looked at the LRR segmented data contained in the file
> “human1mduo-segmented_cna (MD5)” available at this address :
> http://firebrowse.org/?cohort=OV
> I found surprising differences in coverage between samples. For example,
> the sample TCGA-13-0751-01A-01D-0358-06 is not covered (there is no
> segment) on the chromosome 19 from position 24421125 to 32436721. On the
> opposite the sample TCGA-13-0727-01A-01D-0358-06 is covered with a segment
> on chr19 from 24171423 to 32486048. I observed that Since that region
> contains important genes for ovarian cancer such as CCNE1, URI1 and that
> probes are located at these positions. Is it normal and what could explain
> such lack of coverage for some samples.
>
> Best,
> Fab
> On 27 Oct 2014, at 15:40, Hailei Zhang <> wrote:
>
> 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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