Re: [GDAC-users] Methylation data

Subject:   Re: [GDAC-users] Methylation data (more for this subject)
From:   Hailei Zhang <> (more from this sender)
Date:   Jun 19, 2015 10:46

Hi Reza,
 
Here is the description for the methylation data:
 
- GBM.meth.by_max_stddev.data : pick the probe with the max stand standard
deviation for each gene
- GBM.meth.by_mean.data : calculate the mean signal values among each gene
- GBM.meth.by_min_clin_corr.data : pick the probe with the min correlation
with conical data for each gene
- GBM.meth.by_min_expr_corr.data : pick the probe with the min correlation
with mRNAseq data for each gene
 
Best,
Hailei
 
 
On Thu, Jun 18, 2015 at 3:59 PM, Ahmadreza Niavarani <
> wrote:
 
> I am afraid; I do like to use your level 3 data for several reasons.
> Just wondering what's the process performed on each dataset.
> Thanks.
> Reza
>
>
> On Thu, Jun 18, 2015 at 10:42 PM, Hailei Zhang <>
> wrote:
>
>> You can download leve2 data through our standard data run.
>>
>> Best,
>> Hailei
>>
>> On Thu, Jun 18, 2015 at 1:07 PM, Ahmadreza Niavarani <
>> > wrote:
>>
>>> Hi Hailei,
>>> Thanks for recommendation.
>>> Can you please let me how those files have been prepared?
>>> Thanks.
>>> Reza
>>>
>>>
>>> On Thu, Jun 18, 2015 at 8:13 PM, Hailei Zhang <
>>> > wrote:
>>>
>>>> Hi Reza,
>>>>
>>>> Our preprocess pipeline is just used to picked one important probes (
>>>> GBM.meth.by_min_expr_corr.data) or the mean values among probes for
>>>> each gene (GBM.meth.by_mean.data).
>>>>
>>>> If you just want to check several genes in methylation data, I
>>>> suggested you to use probe level methylation data. You can draw the density
>>>> plot for each probes and then pick one probe with most methylated.
>>>>
>>>> Best,
>>>> Hailei
>>>>
>>>> On Thu, Jun 18, 2015 at 10:33 AM, Ahmadreza Niavarani <
>>>> > wrote:
>>>>
>>>>> Hi Hailei,
>>>>>
>>>>> Thanks very much for your kind prompt reply!
>>>>>
>>>>> Can you please explain a bit more why above data should be used.
>>>>>
>>>>> Maybe worth to say I have tried above data, which is missing for, for
>>>>> example, APOBEC1 in 5 out of 31 datasets examined, while these are not
>>>>> missing in the respective "meth.by_mean.data", for instance.
>>>>>
>>>>> Please advise!
>>>>>
>>>>> Best.
>>>>>
>>>>> Reza
>>>>>
>>>>>
>>>>> On Thu, Jun 18, 2015 at 6:40 PM, Hailei Zhang <
>>>>> > wrote:
>>>>>
>>>>>> Hi Reza,
>>>>>>
>>>>>> Here is the document about our methylation preprocess:
>>>>>>
>>>>>>
>>>>>> https://confluence.broadinstitute.org/display/GDAC/Methylation+Preprocessor
>>>>>>
>>>>>> You can use GBM.meth.by_min_expr_corr.data to do your correlation.
>>>>>>
>>>>>> Best,
>>>>>> Hailei
>>>>>>
>>>>>> On Thu, Jun 18, 2015 at 3:29 AM, Ahmadreza Niavarani <
>>>>>> > wrote:
>>>>>>
>>>>>>> Dear Sirs,
>>>>>>>
>>>>>>> I am trying to use TCGA data for correlation of some mutations and
>>>>>>> methylated genes. There are some problems though;
>>>>>>>
>>>>>>> When I download the GBM data (preprocess file:
>>>>>>>  gdac.broadinstitute.org_GBM.Methylation_Preprocess.Level_3.
>>>>>>> 2015040200.0.0.tar), four files can be seen as follows:
>>>>>>>
>>>>>>> - GBM.meth.by_max_stddev.data
>>>>>>> ​​
>>>>>>> - GBM.meth.by_mean.data
>>>>>>> - GBM.meth.by_min_clin_corr.data
>>>>>>> - GBM.meth.by_min_expr_corr.data
>>>>>>>
>>>>>>> I can see that the 3rd and 4th are nearly the same, but can you
>>>>>>> please clarify what are the first three files? The data has some
>>>>>>> similarities and some differences, and I am not sure which file should be
>>>>>>> used.
>>>>>>>
>>>>>>> Appreciate your kind assistance.
>>>>>>>
>>>>>>> Best.
>>>>>>>
>>>>>>> Reza
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> Ahmadreza Niavarani, MD, PhD
>>>>>>>
>>>>>>> Digestive Disease Research Institute
>>>>>>>
>>>>>>> Shariati Hospital, Tehran University of Medical Sciences
>>>>>>> Tehran, Iran
>>>>>>>
>>>>>>> Tel: +98 912 213 4494
>>>>>>>  
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> Ahmadreza Niavarani, MD, PhD
>>>>>
>>>>> Digestive Disease Research Institute
>>>>>
>>>>> Shariati Hospital, Tehran University of Medical Sciences
>>>>> Tehran, Iran
>>>>>
>>>>> Tel: +98 912 213 4494
>>>>>  
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>>
>>> Ahmadreza Niavarani, MD, PhD
>>>
>>> Digestive Disease Research Institute
>>>
>>> Shariati Hospital, Tehran University of Medical Sciences
>>> Tehran, Iran
>>>
>>> Tel: +98 912 213 4494
>>>  
>>>
>>>
>>
>
>
> --
>
> Ahmadreza Niavarani, MD, PhD
>
> Digestive Disease Research Institute
>
> Shariati Hospital, Tehran University of Medical Sciences
> Tehran, Iran
>
> Tel: +98 912 213 4494
>  
>
>
 
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