[R] qvalue

From: alex lam (RI) <alex.lam_at_bbsrc.ac.uk>
Date: Mon 02 Oct 2006 - 16:40:00 GMT

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)

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?

Thanks for your help.

Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Midlothian EH25 9PS

Phone +44 131 5274471
Web http://www.roslin.ac.uk

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