Thanks, Laurent. I got the solution by applying plotLocation() command. Using this one can see that the image plot includes both MMs and PMs. Stephen. Quoting Laurent Gautier <laurent@cbs.dtu.dk>: > On Wed, Jan 21, 2004 at 09:04:16PM +0100, Stephen Nyangoma wrote: > > Hi all, > > I am doing image plots of affy chips but cannot get a good refference > > for interpretations. I have read the manual but all it says is that you > > can examine the quality of the intensities from it. It does not explain > > what is plotted, for example. Does the image plot depict both PM and > > MMMs or just PMs. Are the intensities log transformed? How is it > > constructed? Is it realted to the hist plot (which is just a histogram > > of the logged PM intensities on a chip)? > > > > Thanks for your help. > > > > > > Stephen. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > The images are simply probe intensities at their respective X/Y > coordinates. > The intensity are encoded by colors. *all the probe intensities* in CEL > files are plotted (PM/MM/unknown). One can specify a transformation to > apply on probe intensities prior to color encoding. If I remember right, > the default transformation was set to 'log' not so long ago. The default > coloring is a grey scale. > > Examples of such image plots showing experimental artefacts can be found > in Chapter 4 of 'Analysis of Gene Expression Data, Methods and Software' > (Springer), or in the forthcoming article 'affy - Analysis of Affymetrix > GeneChip data at the probe level' (Bioinformatics, Feb. 2004). > > > Hoping it helps, > > > > Laurent > > > > -- > -------------------------------------------------------------- > Laurent Gautier CBS, Building 208, DTU > PhD. Student DK-2800 Lyngby,Denmark > tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.