 
I am using limma to analyze my array data. In my dataset three contrasts
are relevant, and limma is able to fit these in a single run.
I now would like to use the package multtest to calculate adjusted
p-values (note: i know limma also is able to calculate these but because
of follow-up analyses i now prefer to do this through multtest). 
 
Using the function 'mt.rawp2adjp' I can obtain the adjusted p-values,
but i have to run this function for each contrast seperately:
res1 <- mt.rawp2adjp(fit2$p.value[,1], "BH")
res2 <- mt.rawp2adjp(fit2$p.value[,2], "BH")
res3 <- mt.rawp2adjp(fit2$p.value[,3], "BH") 
 
Since i would like to automate my script, i tried to run multtest with
these arguments:
 
res.ALL <- mt.rawp2adjp(fit2$p.value[,colnames(cont.matrix)], "BH")
 
This function runs fine, but i end up with a single list with a length
of 68070 entries (68070 = 3x 22690; the MOE430A affy array i use
consists of 22690 probesets and i inputted in multtest 3 contrasts).
Obviously, this is not the output i can use. Therefore i would
appreciate to know whether multtest is able to handle multiple contrast
in a single run, and if so, how to perform such analyses.
 
TIA,
Guido
 
targets <- readTargets("targets_A23.txt")
data <- ReadAffy(filenames=targets$FileName)
eset <- rma(data)
TS <- paste(targets$Strain, targets$Treatment, sep=".")
TS <- factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY"))
design <- model.matrix(~0+TS)
colnames(design) <- levels(TS)
fit <- lmFit(eset, design)
cont.matrix <- makeContrasts(WTwyvWTc=WT.WY-WT.Con,
KOwyvKOc=KO.WY-KO.Con, Diff=(WT.WY-WT.Con)-(KO.WY-KO.Con),
levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2)
 
 
res1 <- mt.rawp2adjp(fit2$p.value[,1], "BH")
adjp <- res1$adjp[order(res$index), ]
 
etc
 
 

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
email:      guido.hooiveld@wur.nl 



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