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 ---------------------------------------------------------------------- -------- This email message and any attachments are confidential and ...{{dropped}}

Hi Wenquiong, On Feb 18, 2005, at 5:05 PM, Wenqiong Chen wrote: > 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. Please tell us what platforms you and he are using, what versions of R, and the versions of the packages you are using. You wrote that your friend is using R-1.9.1 and that very well could be the problem. The current released version of Bioconductor requires R-2.0.x. So the first thing to have him try is upgrading to the latest stable R release (or better, yet, R-patched). + seth