[BioC] problem (bug?) and solution for pm function

[Jenny Drnevich]

Hi,

We noticed a problem/change with the affy pm function when going from the 
Drosophila 1 chips to the Drosophila 2.0 chips. I've figure out an easy 
solution, so I thought I'd point out the problem and solution. When working 
with the Dros1 chips, the following commands:

 > pmraw<- pm(raw)
 > write.table(pmraw,"pmraw.csv",quote=F,sep=",", col.names=NA)

would output a csv file with a column of the gene names with probe number 
at the end, along with a column for each chip's pm values. However, when 
the same code is used with the Dros 2.0 chips, instead of the gene names 
and probe numbers, the first column just has the number of the row (1 to 
265,358!). The quick fix I found is to do:

 > gn<-geneNames(raw)
 > pmraw<-pm(raw,gn)
 > write.table(pmraw,file="pmraw.csv",quote=F,sep=",",col.names=NA)

I'm not sure why this change occurred - maybe it has something to do with 
the new binary format of the chips? Would there be any other functions 
(besides mm obviously) that might have similar problems/changes with the 
new chips?

Thanks,
Jenny



Jenny Drnevich, Ph.D.
Department of Animal Biology
University of Illinois
515 Morrill Hall
505 S Goodwin Ave
Urbana, IL 61801
USA

ph: 217-244-6826
fax: 217-244-4565
e-mail: drnevich at uiuc.edu