Hi there, besides the 15 or so different probe set on the hgu95a and hgu95av2 chips, the chips are basically the same. What is the best pratice to mix them in one AffyBatch? Cheers, Hinnerk

Hi Hinnerk, On Tue, 4 Mar 2003, Hinnerk Boriss wrote: > besides the 15 or so different probe set on the hgu95a and hgu95av2 > chips, the chips are basically the same. What is the best pratice to mix > them in one AffyBatch? Not sure what is best practice. One way is by matching the probe sequences and creating a suitable new CDF with only the common probes. This should now have become fairly easy with the "matchprobes" package. It should appear in the "Developmental Packages" section (and yes, it is developmental). In its subdirectory inst/example there is a file combine_demo.R which seems to do what you want. You can also look at the code via the developer page: http://franz.stat.wisc.edu/cgi- bin/viewcvs.cgi/Rpacks/matchprobes/?cvsroot=Bioconductor#dirlist Best regards Wolfgang ---------------------------------------- Wolfgang Huber w.huber@dkfz.de Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany ----------------------------------------