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

[Rafael A. Irizarry]

are you sure this is not a diffeence between two version of the affy
package? 

in the latest version (1.4.x) we made a change to make the "pm"
method faster when you want all the pms back. 
the drawback is you dont get the
rownames as before. if you want the rownames you can use:

probes(raw,"pm")
or
pm(raw,genenames=genaNames(raw))

sorry about any inconvinience this has caused.


On Mon, 12 Jul 2004, Jenny Drnevich wrote:

> 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
> 
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