[BioC] QQ plot 450k data

[James W. MacDonald]

Hi Khadeeja,

I don't think you can conclude much at all from a QQ plot, other than 
the obvious that the observed p-values don't follow the expected 
distribution. There can be any number of things that could cause that, 
including systemic differential methylation (e.g., there really might be 
lots of differences in the methylation between your samples).

Best,

Jim


On 5/20/2014 12:40 PM, khadeeja ismail wrote:
> Thank you very much. I was suggested QQ plots to look for biases in 
> two different analysis.
>
> One seem to have a uniform distribution while the other seem to 
> deviate much. Probably due to different global methylation profiles? 
> Can I conclude from it that there is a bias?
>
> Thanks again,
> Khadeeja
>
>
> On Tuesday, May 20, 2014 5:14 PM, James W. MacDonald <jmacdon at uw.edu> 
> wrote:
>
>
> 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
> >
> > Email: m.a.rijlaarsdam at gmail.com <mailto:m.a.rijlaarsdam at gmail.com>
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> > Website: http://www.martinrijlaarsdam.nl 
> <http://www.martinrijlaarsdam.nl/>
> >
> >
> > On Tue, May 20, 2014 at 3:48 PM, James W. MacDonald <jmacdon at uw.edu 
> <mailto: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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>
> >>
> >     [[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
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099