[BioC] how to separate probe numbers from AffyIDs?

[Rafael A. Irizarry]

the probeNames method gives you the probeNames in the same ordering as the 
pm method (if you use the default cdfenvironments). within a probe set  
the pms are ordered by probe number (position along the transcript). 
probeNames has an "mm" argument that if made TRUE does the same for the 
MM probes.

example:
library(affydata)
data(Dilution)
pms <- pm(Dilution)
pmnames <- probeNames(Dilution)

you dont have to save the numbers because they are already ordered. for 
exmaple, for probe "1001_at", you can see a table of the values you want 
by doing the equivelant in SAS to:

Index <- which(pmnames=="1001_at")
data.frame(pm=pms[Index],names=pmnames[Index],number=seq(along=Index))


Tue, 15 Jul 2003, Jenny Drnevich wrote:

> Hello,
> 
> I've been using Bioconductor to do the background correction and 
> normalization of my data, but I want to use the probe values themselves 
> instead of a summary value for my statistical analyses. I am able to export 
> the matrix of pm values, but the first column lists the AffyID and probe 
> number together (e.g., 100_g_at1, 100_g_at2, 100_g_at3, etc.). Is there an 
> easy way to separate these? I need two columns: one with just the AffyID 
> (100_g_at) and one with the probe number (1, 2, 3, etc.).  I don't need 
> these two columns in the pm matrix I export, because I can combine the two 
> in SAS.
> 
> Thanks in advance,
> Jenny
> 
> Jenny Drnevich, Ph.D.
> Department of Animal Biology
> 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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