[BioC] combine pm and oligo sequence information

[James W. MacDonald]

Wang, Yonghong (NIH/NCI) wrote:
>  >i.pm <- indexProbes(data, "pm");
> 
> 
>>xy.pm <- indices2xy(i.pm, abatch = data);
> 
> 
>>seq.pm <- u133x3pprobe$RESIDUES[(xy.pm[,1] == u133x3pprobe$POSITIONX +1)&
> 
> (xy.pl[,2] == u133x3pprobe$POSITIONY + 1)];


i.pm <- unlist(indexProbes(data, "pm"))
## note here that 'data' is a poor choice for a variable name
## you are masking an existing function. dat or Data would be better

## convert X and Y values to indices
i.pt <- xy2i(u133x3pprobe$x, u133x3pprobe$y)
## match the affybatch order to the probe table order
index <- match(i.pm, i.pt)
## extract sequence
seqnc <- u133x3pprobe$sequence[index]
write.table(cbind(probeNames(data),pm(data),mm(data), 
seqnc),file="mytest.dat",sep = "\t")

HTH,

Jim


> 
>  
> 
> Y. Wang
> 
> ATC/NCI/NIH
> 
>  
> 
> 
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> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623