[BioC] order of PM from ReadAffy and probe$sequence

[Wolfgang Huber]

Lana Schaffer wrote:
> I am matching the PM and MM intensities from ReadAffy to the probe$sequence from
> the matchprobes package and not 100% sure that the order of the intensities are in
> the same order as probes in the metadata probe file.  The list of probe ids might be
> possible from the probeset class but I don't know how to get the probe ids equivalent
> to the probe$sequence or the probe file.
> Lana

Try

library(hgu95av2cdf)
? i2xy

Try also

plot(sort(xy2i(hgu95av2probe$x, hgu95av2probe$y)), pch=".")

with and without "sort" to see what's going on.

Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber