Dear all, I am a new user of bioconductor. I use MAS function in the Affy package to convert CEL file to XLS file. But the result dose not agree with that by MAS 5.0. Does anyone ever have such problem and have any advise. Any help is greatly appreciated Thank you very much Lang Chen Research Assistant Department of Biostatistics Section on Statistical Genetics Ryals Public Health Building, Suite 343A University of Alabama at Birmingham 1530 3rd Ave S Birmingham, Alabama 35294 Tel 205-9757772

Lang Chen <lchen@ms.soph.uab.edu> writes: > I am a new user of bioconductor. I use MAS function in the Affy package to > convert CEL file to XLS file. But the result dose not agree with that by MAS > 5.0. Does anyone ever have such problem and have any advise. Yes. What is the level of disagreement that you observe? Ignorable, mild, severe? best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ -------------------- FHCRC:Tu: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (CHANGE: monday/wednesday/friday locations are completely unpredictable.)

Hi Lang Chen (and to anyone else this is an issue for), We have made our best attempts to duplicate the MAS 5.0 algorithm using available documentation. As you might appreciate, sometimes algorithms are not as fully documented as one might hope and it is possible that there are implementation details that Affymetrix uses that are not in the documentation. It would be helpful if you could tell us what the level of disagreement is. Also it would be most useful to let us know the exact function call you used to generate your ExprSet to make sure you are really doing what you think that you are doing. Thanks, Ben > Dear all, > > I am a new user of bioconductor. I use MAS function in the Affy package to > convert CEL file to XLS file. But the result dose not agree with that by MAS > 5.0. Does anyone ever have such problem and have any advise. > > Any help is greatly appreciated > > Thank you very much > > Lang Chen > > Research Assistant > Department of Biostatistics > Section on Statistical Genetics > Ryals Public Health Building, Suite 343A > University of Alabama at Birmingham > 1530 3rd Ave S > Birmingham, Alabama 35294 > Tel 205-9757772 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

> -----Original Message----- > From: Ben Bolstad [mailto:bolstad@stat.berkeley.edu] > Sent: Thursday, March 06, 2003 5:48 PM > To: Lang Chen > Cc: 'bioconductor@stat.math.ethz.ch' > Subject: Re: [BioC] the result of bioconductor not agree with MAS > > > Hi Lang Chen (and to anyone else this is an issue for), > > We have made our best attempts to duplicate the MAS 5.0 > algorithm using > available documentation. If I read the code in pmcorrect.mas() correctly (affy version 1.1), the mismatch is not subtracted from the perfect match, so the line pm.corrected <- applycbindpps.pm, pps.im, delta), 1, max) should IMHO rather read pm.corrected <- applycbindpps.pm-pps.mm, pps.im-pps.mm, delta), 1, max) ? I might very well be missing something, so if somebody could give me a clue I'd be grateful. Best regards Johannes

> If I read the code in pmcorrect.mas() correctly (affy version 1.1), > the mismatch is not subtracted from the perfect match, so the line > > pm.corrected <- applycbindpps.pm, pps.im, delta), 1, max) > > should IMHO rather read > > pm.corrected <- applycbindpps.pm-pps.mm, pps.im-pps.mm, delta), 1, > max) ? > > I might very well be missing something, so if somebody could give > me a clue I'd be grateful. This issue was corrected a long time ago, I believe the release version 1.1.1 of affy had the fix. Ben

OK, I saw it now in http://www.dkfz.de/bioconductor/changelog.html in the message of Dec 8th, 2002. Sorry to mention bugs without downloading the most recent version first. Greetings Johannes