[BioC] affy and simpleaffy error

[Narendra Kaushik]

I am having problem with updating affy package, getting message:
cannot open compressed file 'C:/PROGRA~1/R/R-22~1.0DE/library/affy/R/all.rda' 
Error in library(affy) : .First.lib failed for 'affy' 

(run on windowsxp prof. R 2.2.0 dev and all packages are dev)

Running simpleaffy package I get message: 
raw.data <- read.affy("covdesc.txt") #read data in working directory 
> x.rma <- call.exprs(raw.data, "rma") # Creates expression values
Background correcting
Normalizing
Calculating Expression
> write.exprs(x.rma, file="rma_affy_all.txt")
> results <- pairwise.comparison(x.rma, "animal", c("1", "2"), raw.data)
Getting probe level data...
Computing p-values
Error in as.double(pms[, x]) : subscript out of bounds 

Thanks for help.

Narendra 

Narendra Kaushik
School of Biosciences, 
University of Cardiff, 
Cardiff CF10 3US
kaushiknk at cardiff.ac.uk