Hello: I am new to bioconductor. Recently, I am trying to generate a file
which will contain probeset id, pm, mm intensities and oligo sequence
information (and/or positions) for all the oligo on the affy chip. I
searched the bioconductor mailing archive, found one response quite helpful,
but still couldn't work out. Here is what I did. I am using u133x3p chip and
have download the cdf and probe library into the R session. Before I
started, I also put all the .CEL file in my working directory.

 

>setwd("c:/R_file");

>library(affy);

>data <- ReadAffy();

>library(matchprobes);

>library(u133x3pcdf);

>library(u133x3pprobe);

 

Using the code below, I can retrieve the pm and mm intensities as well as
probeset id information

 

>write.table(cbind(probeNames(data),pm(data),mm(data)),file="mytest.dat",sep
="\t");

 

The question is how I can include the sequence information in the output
file.

 

Based on the code I got from mailing list, I am thinking about using the
code below to retrieve the sequence information (give error message). As I
am still quite confused about some usage of some function, could someone
there give me a help:

 >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)];

 

Y. Wang

ATC/NCI/NIH

 


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