[BioC] pamr / R graphics recording

[Katleen De Preter]

Hello,

I'm trying to use the pamr package on Affymetrix RMA normalised data. 
Pamr.train-function works on the data. However, I got following errors 
with pamr.plotcen and pamr.listgenes. Do anyone know what may be the 
problem?
And another (R-related) question: how can I automatically (before 
starting a script) record all generated graphes???

 > pamr.plotcen(mData.train, mData.data, threshold=4.0)
Error in text(xy.coords(x, y, recycle = TRUE), labels, adj, pos, offset,  :
        zero length 'labels'

 > pamr.listgenes(mData.train, mData.data, threshold=4.0)
Error in pamr.listgenes(mData.train, mData.data, threshold = 4) :
        length of dimnames [2] not equal to array extent

used R-SCRIPT:
library(pamr)
library(affy)
load("C:/Documents and Settings/Katleen/Mijn documenten/WERK/Analyse 
affymetrix/analyse ALLE CEL FILES/R/nbNBdata.RData")
NBselect<-nbNBdata[,nbNBdata$classnameb%in%c("NB1","NB2B","NB2A")]
classname <- pData(phenoData(NBselect))$classnameb
mData.data <- pamr.knnimpute(list(x = exprs(NBselect), y = classname))
mData.train <- pamr.train(mData.data)
mData.results<- pamr.cv(mData.train, mData.data)
pamr.plotcv(mData.results)
pamr.confusion(mData.results, threshold=4.0)
pamr.plotcvprob(mData.results, mData.data, threshold=4.0)
pamr.plotcen(mData.train, mData.data, threshold=4.0)
pamr.geneplot(mData.train, mData.data, threshold=5.3)
pamr.listgenes(mData.train, mData.data, threshold=4.0)

Best regards,

Katleen


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