[BioC] QQ plot 450k data

[James W. MacDonald]

Hi Martin,

That's exactly what you would expect to see, which is why you do a QQ 
plot in the first place. On one axis you plot the expected (uniform) 
distribution of p-values, and on the other axis you plot the observed 
p-values. The p-values that deviate from the expectation are then 
possible true positives.

Best,

Jim


On 5/20/2014 9:51 AM, Martin Rijlaarsdam wrote:
> Hi Jim,
>
> Jim, if (groups) of samples differ in their global methylation profile
> (i.e. the majority of probes significantly differs in one direction), would
> you not expect to see a deviation from this uniform distribution then?
>
> Best,
> Martin
>
>
> --
> M.A. (Martin) Rijlaarsdam MSc. MD
> Erasmus MC - University Medical Center Rotterdam
> Department of Pathology
> Room Be-432b
> Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
> Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
>
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>
>
> On Tue, May 20, 2014 at 3:48 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
>
>> Hi Khadeeja,
>>
>> The distribution of p-values under the null hypothesis should always be
>> uniform.
>>
>> Best,
>>
>> Jim
>>
>>
>> On 5/19/2014 5:14 PM, khadeeja ismail wrote:
>>
>>> Hi All,
>>>
>>> What would be the right distribution to use as expected p values in a QQ
>>> plot for results from 450k analysis? I have been searching, but not able to
>>> find in mentioned anywhere.
>>>
>>>
>>> Thanks in advance,
>>>
>>> Khadeeja
>>>          [[alternative HTML version deleted]]
>>>
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>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099