[BioC] Pm problem

[Wenqiong Chen]

Hi, all:
My friend is working with the same custom Genechip as the one I am
working. While everything worked in my computer, he has been not very
lucky and I can't figure out why. Here is what we are doing. We are
trying the get the pm values for a subset of genes on the chip. He has
successfully built his own cdf package, but after that he kept getting
the same error message.

coelicolor.genes<-read.table("Scotable4R.txt",header=T,sep="\t")
#read in a data frame with 1st column the name of gene list
> dim(coelicolor.genes)
[1] 7726    5
> library(affy)
> M600affy<-ReadAffy()
> M600affy
AffyBatch object
size of arrays=712x712 features (142586 kb)
cdf=diS_div712a (17798 affyids)
number of samples=36
number of genes=17798
annotation=disdiv712a
> pm.coelicolor<-pm(M600affy,coelicolor.genes[,1])
Error in mget(x, envir, mode, ifnotfound, inherits) : 
        invalid first argument

What could possibly be wrong? He is using R1.9.1 on either his Unix
machine or windows, and the error message was the same.
Thanks
wenqiong


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