Re: [R] qvalue

From: Uwe Ligges <ligges_at_statistik.uni-dortmund.de>
Date: Mon 02 Oct 2006 - 16:52:53 GMT

alex lam (RI) wrote:
> Dear colleagues,
>
> This is not strictly a R question, but I hope it is ok to ask on the
> list.
> I fed a vector of p-values from about 20 million anova tests to the
> package q-value and obtained this output:
>

>> qsummary(asso_p.qvalue)

>
> Call:
> qvalue(p = asso_p.vec)
>
> pi0: 1
>
> Cumulative number of significant calls:
>
> <1e-04 <0.001 <0.01 <0.025 <0.05 <0.1 <1
> p-value 22711 59067 262103 551316 1013241 1936797 20048103
> q-value 3554 5211 9275 12807 16951 24557 20048103
>
> I can see that there are many hits with very small q-values ,say q
> <0.001, so to use that as cut off I have 5211 significant hits and can
> expect ~ 5 false postives. But my pi0 is 1. Does it mean that all my
> tests are true null and there are no significant results?

Well, yes, at least under H0 you would expect the above results in such a case.
Concluding without further information that *all* are non-significant is impossible, though. This requires some interpretation depending on where the tests some from...

Uwe Ligges

> Thanks for your help.
> Alex
>
> ------------------------------------
> Alex Lam
> PhD student
> Department of Genetics and Genomics
> Roslin Institute (Edinburgh)
> Roslin
> Midlothian EH25 9PS
>
> Phone +44 131 5274471
> Web http://www.roslin.ac.uk
>
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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Tue Oct 03 02:55:35 2006

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