[BioC] Multtest package

[Ramon Diaz-Uriarte]

Dear Claire,

As the program is telling you ("We'll do complete enumerations"), it is using 
complete enumeration, because, it would seem, all Bs you are using are larger 
than 20. Sensibly, the program will use complete enumeration whenever B > 
number of permutations under complete enumeration.

Hope this helps,

Ramón




On Tuesday 19 August 2003 13:43, Claire Wilson wrote:
> Dear all,
>
> I have been looking at using the multtest package for multiple testing
> correction. specifically on page 5 of the vignette, I have been trying to
> calculate maxT adjusted p-values for Affymetrix data.  However the function
> will only run a 20 permutations, irrespective of what I set B to.
>
> > tmp1 <- eset at exprs
> > class(tmp1)
>
> [1] "matrix"
>
> > dim(tmp1)
>
> [1] 22690     6
>
> > temp.cats
>
> [1] 0 0 0 1 1 1
>
> > resT <- mt.maxT(tmp1, temp.cats)
>
> We'll do complete enumerations
>
> We're doing 20 complete permutations
> b=1     b=2     b=3     b=4     b=5     b=6     b=7     b=8     b=9    
> b=10
>
> b=11    b=12    b=13    b=14    b=15    b=16    b=17    b=18    b=19   
> b=20
>
> > resT <- mt.maxT(tmp1, temp.cats, B=100000)
>
> We'll do complete enumerations
>
> We're doing 20 complete permutations
> b=1     b=2     b=3     b=4     b=5     b=6     b=7     b=8     b=9    
> b=10
>
> b=11    b=12    b=13    b=14    b=15    b=16    b=17    b=18    b=19   
> b=20
>
>
> When I did the example in the vignette, everything worked fine, with the
> number of permutations equal to B or the default if B was not set.
>
> Any ideas?
>
> Thanks
>
> Claire
>
> --
> Claire Wilson, PhD
> Bioinformatics group
> Paterson Institute for Cancer Research
> Christies Hospital NHS Trust
> Wilmslow Road,
> Withington
> Manchester
> M20 4BX
> tel: +44 (0)161 446 8218
> url: http://bioinf.picr.man.ac.uk/
>
> --------------------------------------------------------
>
>
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>
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-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://bioinfo.cnio.es/~rdiaz