[BioC] how to separate probe numbers from AffyIDs?

[Marcus Davy]

Another lternative is to use base package functions using regular expressions and substring to break the AffyID information up into the two vectors.e
 .g.

library(affydata)
data(Dilution)
pms <- pm(Dilution)
AffyInfo <- dimnames(pms)[[1]]

cutpos <-  regexpr("\\d+$",AffyInfo, perl=T)

# Under help(regexpr)
#`perl=TRUE' will only be available if R was compiled against 
#     PCRE: this is detected at configure time.  All Unix and Windows
#     system should have it.

AffyID <- substr(AffyInfo, 1, cutpos-1)
probe  <- as.numeric(substr(AffyInfo,cutpos, nchar(AffyInfo)))

cbind(AffyInfo, AffyID,probe)[1:20,]


marcus


>>> Jenny Drnevich <drnevich at uiuc.edu> 16/07/2003 4:15:30 AM >>>
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 exportt
 he 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 ane
 asy 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 twoi
 n 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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