Hi terdon,

You are absolutely right. I apologize for any inconvenience my lack of
coffee might have caused :-)

I simulated some p-values with the length of your vector and ran the
p.adjust() function on them. Here is what I got:

system.time(res <- p.adjust(pv, method = 'fdr'))
   user  system elapsed
184.529   4.862 192.066

If you wish, I can run that for you on my machine. Below is my sessionInfo()

R version 2.11.1 Patched (2010-05-31 r52180)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] multtest_2.6.0 Biobase_2.8.0

loaded via a namespace (and not attached):
[1] MASS_7.3-7      splines_2.11.1  survival_2.36-2 tools_2.11.1


Best,
Jorge


On Tue, Mar 8, 2011 at 10:37 AM, terdon <> wrote:

> Hi Jorge, and thanks for your answer, it looks promising.
>
> However, I have a question. First of all, I am a lowly biologist so please
> excuse any horrible errors of understanding I may make.
>
> So, the BH correction depends on, among other things, sorting the vector of
> P-values from the smallest to the largest and then multiplying each value
> by
> the length of the vector times its rank.
>
> If I understand correctly, your suggestion is to use  p.adjust on a subset
> of the vector pv, set the n parameter to the length of the entire vector
> and
> then iterate until all P-values have been adjusted.
>
>  Wouldn't I still need to know the rank of each p value in the subset
> vector
> with respect to its position in the original sorted vector? I can see how
> to
> calculate that of course, but how can I give this info to p.adjust if it
> only takes the length of the vector as an argument?
>
> Thanks again
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Multiple-testing-corrections-on-very-large-vector-tp3341398p3341615.html
> Sent from the R help mailing list archive at Nabble.com.
>
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