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

[Jenny Drnevich]

You're right - I also changed versions of Bioconductor as well as Dros 
chips.  Your second solution is the same as mine, except in one line. I did 
notice that "pm" works much faster now!

Thanks,
Jenny

At 02:16 PM 7/12/2004 -0400, Rafael A. Irizarry wrote:
>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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >

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