[R] qvalue

[alex lam (RI)]

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?

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