You used the background correction method that subtracts MM values to the corresponding PM values, as Wolfgang mentioned it. The fact that MM are sometimes greater than the PM annoyed enough people to make them consider alternative ways of going through (the simpliest being probably to ider thand igne thess) The forthcoming next release of the package affy will offer few different ways to deal with PMs (and eventually MMs). It is called 'pmcorrect' (as background correction is now used to call a chip wide signal correction) Hopin' it helps, L. -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent On Fri, Nov 08, 2002 at 11:11:29PM +0100, Wolfgang Huber wrote: > Hi Guangchun > > What's wrong with negative values? It may just mean that for these genes the > MM signal is higher than the PM signal, perhaps because your complex mRNA > contains transcripts that match those MM's better than the PM's. Negative > PM-MM values that are not too far from zero may also be just because of > random fluctuations. > Best regards > Wolfgang > > > w.huber@dkfz.de > http://www.dkfz.de/abt0840/whuber > Tel +49-6221-424709 > Fax +49-6221-42524709 > DKFZ, Division of Molecular Genome Analysis > 69120 Heidelberg, Germany > > -----Original Message----- > From: bioconductor-admin@stat.math.ethz.ch > [mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Song, > Guangchun > Sent: Friday, November 08, 2002 11:01 PM > To: 'Bioconductor@stat.math.ethz.ch' > Subject: [BioC] [BioC]Li.Wong expression values < 0? > > > Hi, > > Has anyone gotten negative expression values when using li.wong > normalization by Affy? What the negative values mean? > > Here are what I did: > > > mouse <- ReadAffy() > > liwong = express(mouse, bg=subtractmm, summary.stat=li.wong) > > write.exprs(liwong,file="LiWong.txt") > > The min = -2358.292881, and max = 8763.940708. > > > Guangchun > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor