Dear experts, I am a beginner in working with R/Bioconductor. At the moment I try to get familiar with microarray analysis. When loading the Estrogen-Data into an AffyBatch, the number of probes of an array is 640*640=409600. If I calculate the overall amount of pm and mm-values for all probesets of an array, I get as result 2*201800=403600. What is an explanation for this difference or what are the other probes necessary for? I'll appreciate suggestions on this question. Thanks. Regards, Bernd Holleczek -- Bernd Holleczek <bernd.holleczek@gmx.de> HoHoHo! Seid Ihr auch alle schön brav gewesen? GMX Weihnachts-Special: Die 1. Adresse für Weihnachts- männer und -frauen! http://www.gmx.net/de/cgi/specialmail

On Sun, Nov 30, 2003 at 09:50:07PM +0100, Bernd Holleczek wrote: > Dear experts, > > I am a beginner in working with R/Bioconductor. At the moment I try to get > familiar with microarray analysis. > > When loading the Estrogen-Data into an AffyBatch, the number of probes of an > array is 640*640=409600. > If I calculate the overall amount of pm and mm-values for all probesets of > an array, I get as result 2*201800=403600. > > What is an explanation for this difference or what are the other probes > necessary for? There are probes that are not PMs nor MMs. For what we know, some of them are used to align a grid during the image analysis step. A cute example dealing with these "unknown" probes can be found in an article about the affy package (Bioinformatics, in press). Hopin' it helps, L. > > I'll appreciate suggestions on this question. > Thanks. > > Regards, > > Bernd Holleczek > > -- > Bernd Holleczek <bernd.holleczek@gmx.de> > > HoHoHo! Seid Ihr auch alle sch?n brav gewesen? > > GMX Weihnachts-Special: Die 1. Adresse f?r Weihnachts- > m?nner und -frauen! http://www.gmx.net/de/cgi/specialmail > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent