Hello, I did some Spatial plot using the following R code: maImage(christian.raw[,1], x="maGf") for green foreground or maImage(christian.raw[,1], x="maGb") for green backgound This works perfectly. Now for diagnostic purposes I want to compare foreground to background intensities. The problem is that the intensity scale of the plot (indicated in each plot on the right where colour is correlated to intensity) is done automatically and of course varies between fore- and background. Is there a way to adjust the scale manually? Thanks, Francis [[alternative HTML version deleted]]

Francis You just need to add a zlim parameter to your maImage call. For example, if the minimum expression is 20 (across foreground and background) and the max expression is 10000 (again, across foreground and background), issuing the commands: maImage(christian.raw[,1],x="maGf",xlim=c(20,10000)) and maImage(christian.raw[,1],x="maGb",xlim=c(20,10000)) Will get you plots that have the same scale varying from 20 to 10000. Sean -- Sean Davis, M.D., Ph.D. Clinical Fellow National Institutes of Health National Cancer Institute National Human Genome Research Institute Clinical Fellow, Johns Hopkins Department of Pediatric Oncology -- On 1/13/04 11:23 AM, "Foata,Francis,LAUSANNE,NRC/N&H" <francis.foata@rdls.nestle.com> wrote: > Hello, > > I did some Spatial plot using the following R code: > > maImage(christian.raw[,1], x="maGf") for green foreground > or > maImage(christian.raw[,1], x="maGb") for green backgound > This works perfectly. > > Now for diagnostic purposes I want to compare foreground to background > intensities. The problem is that the intensity scale of the plot (indicated > in each plot on the right where colour is correlated to intensity) is done > automatically and of course varies between fore- and background. > > Is there a way to adjust the scale manually? > > Thanks, > > Francis > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >