[BioC] Multtest package

[Claire Wilson]

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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