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Hi Eric, Thanks for the clear documentation of the commands that can lead to the solution of my problem. Regards. Stephen. On Mon, 2003-06-30 at 15:17, Eric wrote:Hi, Rafael Irizarry was kind enough to walk me through this, and it worked as of May of this year. The text is here in the discussions thread (https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-April/00126 9.html) Then you can use the write.table command to generate text files if you want to export the values to other programs. HTH, -E When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioconductor digest..." Today's Topics: 1. obtaining PM/MM data from the .CEL files (Stephen Nyangoma) 2. Re: obtaining PM/MM data from the .CEL files (James MacDonald) ---------------------------------------------------------------------- Message: 1 Date: 28 Jun 2003 12:49:25 +0200 From: Stephen Nyangoma <s.nyangoma@cs.rug.nl> Subject: [BioC] obtaining PM/MM data from the .CEL files To: bioconductor@stat.math.ethz.ch Message-ID: <1056797365.1728.6.camel@iwi142> Content-Type: text/plain Hi I am just beginning my research in the analysis of Oligonucleotide GeneChip data. I have difficulty getting information from the data bases. I have been given some .CEL files and I need to extract perfect match (PM)/mismatch (MM) pair signal intensities. Where can I get information how to do this? Where can I get good information about extracting info from .CEL files? Best regards. Stephen. ------------------------------ Message: 2 Date: Sat, 28 Jun 2003 11:28:35 -0400 From: "James MacDonald" <jmacdon@med.umich.edu> Subject: Re: [BioC] obtaining PM/MM data from the .CEL files To: <s.nyangoma@cs.rug.nl>, <bioconductor@stat.math.ethz.ch> Message-ID: <sefd7be6.035@mail-01.med.umich.edu> Content-Type: text/plain; charset=US-ASCII You can get information from the help pages that come with R. Type help.start() to get a browser, and go to the affy help section. Additionally, you can get information from the vignettes that come with affy. You will find links to the vignettes at the top of the affy help page, or you can type openVignette() after library(affy) from within R. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Stephen Nyangoma <s.nyangoma@cs.rug.nl> 06/28/03 06:49AM >>> Hi I am just beginning my research in the analysis of Oligonucleotide GeneChip data. I have difficulty getting information from the data bases. I have been given some .CEL files and I need to extract perfect match (PM)/mismatch (MM) pair signal intensities. Where can I get information how to do this? Where can I get good information about extracting info from .CEL files? Best regards. Stephen. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 4, Issue 51 ******************************************* Eric Blalock, PhD Dept Pharmacology, UKMC 859 323-8033 STATEMENT OF CONFIDENTIALITY The contents of this e-mail message and any attachments are confidential and are intended solely for addressee. The information may also be legally privileged. This transmission is sent in trust, for the sole purpose of delivery to the intended recipient. If you have received this transmission in error, any use, reproduction or dissemination of this transmission is strictly prohibited. If you are not the intended recipient, please immediately notify the sender by reply e-mail or at (859) 323-8033 and delete this message and its attachments, if any. > ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor