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
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On Tue, May 20, 2014 at 3:48 PM, James W. MacDonald <jmacdon@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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