[BioC] p.adjust returns one uniform value

[Jenny Drnevich]

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
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ph: 217-244-7355
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e-mail: drnevich at uiuc.edu