[BioC] p.adjust returns one uniform value

[Benjamin Otto]

Hi Jenny,

Thanks for the thorough answer. I checked my distributions yesterday and
indeed they looked very different to my usual ones, smallest pvalue 0.0004
but about 54000 probesets. :)

Best regards

Benjamnin



-----Ursprüngliche Nachricht-----
Von: Jenny Drnevich [mailto:drnevich at uiuc.edu] 
Gesendet: Tuesday, September 04, 2007 6:19 PM
An: Benjamin Otto; bioconductor at stat.math.ethz.ch
Betreff: Re: [BioC] p.adjust returns one uniform value

Hi Benjamin,

There's nothing wrong with p.adjust(), it's your data - there aren't enough
genes with low raw p-values. In the BH (fdr) adjustment, you basically take
the smallest raw p-value and multiply it by n, the number of genes, to get a
temporary adjusted p-value, then you take the second smallest raw p and
multiply it by n-1, etc., up the line creating temporary adjusted p-values.
When a higher ranking temporary p-value is lower than ones below it, all the
p-values below it get replaced with that value as the final adjusted
p-value. The largest raw p-value is only multiplied by 1 and in this data
set of yours,  this is the lowest temporary adjusted p-value for ALL the
genes, which is why you're seeing only one uniform "adjusted p-value".

Cheers,
Jenny

At 10:23 AM 9/4/2007, Benjamin Otto wrote:
>Hi,
>
>I'm just sticking on a strange problem. For a set of p-values a 
>correction via p.adjust should be calculated. Strangely the function 
>returns one uniform "adjusted p-value" for all genes although the range 
>of the raw p-values goes from 0.00043 to 0.99. For BH it is something 
>around 0.996 and for holm, bonferroni etc. it is 1.
>
>The function produces nice values for the examples and I used to use 
>the function frequently before without ever observing such behaviour. 
>Any suggestions?
>
>Benjamin
>
>
>R version 2.5.0 (2007-04-23)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>States.1252;LC_MONETARY=English_United
>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>attached base packages:
>[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
>"base"
>
>other attached packages:
>mouse4302
>  "1.16.0"
>
>======================================
>Benjamin Otto
>University Hospital Hamburg-Eppendorf
>Institute For Clinical Chemistry
>Martinistr. 52
>D-20246 Hamburg
>
>Tel.: +49 40 42803 1908
>Fax.: +49 40 42803 4971
>======================================
>
>
>
>--
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist W.M. Keck Center for
Comparative and Functional Genomics Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
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ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu 




-- 
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):

Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg

Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Ricarda Klein
Prof. Dr. Dr. Uwe Koch-Gromus