[BioC] qvalue package: Strange distribution of q values

[Dr. Reinhard Hoffmann]

Dear list,
I noticed a strange distribution of  q values after correcting a list of 
22960  p values with the q value package:

 > qsummary(q)

Call:
qvalue(p = p, robust = T)

pi0:    0.07742146     

Cumulative number of significant calls:

        <1e-04 <0.001 <0.01 <0.025 <0.05  <0.1    <1
p-value    293   1067  3104   4634  7247 12082 22689
q-value      0    567  4901  17702 21382 22690 22690

As you can see, starting with a cutoff of < 0.01, the number of 
significant q values is higher than the number of significant p values, 
which, in my mind, should not be the case. The p value distribution 
looks ok (see attached histogram). I have also attached the q value 
plots and the p value vector for information.

Any suggestions why these q values behave the way they do?
Greetings Reinhard

-- 
Dr. Reinhard Hoffmann
Max-von-Pettenkofer-Institut
Pettenkoferstr. 9a
80336 München
Germany
Phone: +49-89-5160-5424 (office), -5246 (Lab)
Fax: +49-89-5160-5223
Mobile: +49-171-5169923
Email: r_hoffmann at mvp.uni-muenchen.de

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