Hello, I am running RHEL 3, R 2.2, BioC 1.7, gcrma2.2 I would like to apply gcrma to a custom chip, but I don't know how to tell gcrma to look on my local box for the probe sequence information. If anyone knows how to do this, I would appreciate any assistance you can give. Dan

I think what you need is a file called chipname_probe_tab, as an example, HG-U95Av2_probe_tab is for HG_U95Av2. I have the same problem when I ran gcRMA with our custom chips. gcRMA wouldn't run. I am waiting for that table file to arrive so I can give it a try. If what I said is not correct, please feel free to correct me. I would like to know this as well. Regards, Johnny -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Daniel Pick Sent: Friday, November 11, 2005 12:16 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] GCRMA with custom chips Hello, I am running RHEL 3, R 2.2, BioC 1.7, gcrma2.2 I would like to apply gcrma to a custom chip, but I don't know how to tell gcrma to look on my local box for the probe sequence information. If anyone knows how to do this, I would appreciate any assistance you can give. Dan _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Daniel Pick wrote: > Hello, > I am running RHEL 3, R 2.2, BioC 1.7, gcrma2.2 > I would like to apply gcrma to a custom chip, but I don't know how to tell > gcrma to look on my local box for the probe sequence information. If > anyone knows how to do this, I would appreciate any assistance you can > give. First you have to make a probe package (have you done this?). If not, you have to use makeProbePackage() in the matchprobes package. Leave pkgname set to NULL so the package will get the correct name. After making the package, install using R CMD INSTALL, and you should be good to go. HTH, Jim > > Dan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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