[BioC] help with affypdnn

[Anthony Bosco]

Hi.

I am trying to use expressopdnn function to generate expression measure.

The commands that I use are listed below, the calculations take a 
very long time (therefore takes ages to trouble shoot) but only 
return NA values.

If I substitute exampleData, with my data it doesn't work at all.

Can someone please help.


library(affy)
library(affypdnn)
library(hgu133aprobe)
library(matchprobes)

data<-ReadAffy()

energy.file<-system.file("exampleData","pdnn-energy-parameter_hg-u133a.txt",package="affypdnn")

params.chiptype<-pdnn.params.chiptype(energy.file,probes.pack="hgu133aprobe")

data.pdnn<-expressopdnn(data,bg.correct=FALSE,normalize.method="quantiles",params.chiptype=params.chiptype)

data.pdnnpredict<-expressopdnn(data,bg.correct=FALSE,normalize.method="quantiles",pmcorrect.method="pdnnpredict",params.chiptype=params.chiptype)

-- 
______________________________________________

Anthony Bosco - Cell Biology Research Assistant

Institute for Child Health Research
(Company Limited by Guarantee ACN 009 278 755)
Subiaco, Western Australia, 6008

Ph 61 8 9489  , Fax 61 8 9489 7700
email anthonyb at ichr.uwa.edu.au