Hi, I'm still fairly new to all this so this may be a simple question. I have a problem sometimes when using the plotDensities function in Limma, in some cases the plot produced is on such a scale that the lines are not distinguishable. Usually the intensity axis is in the range of -10 :30, however ocassionally after a printtip lowes normalisation, or some betweenArrayNormalizations, the scale of the graph is -5000:10000 with the density peak being a single spike in the middle of the plot. Is there a way to control the axis scale? or is there an easy way to set a minimum and maximums for an MA object? Many thanks Pete

Hi Pete, plotDensities() and most plotting functions will take the graphical parameters 'xlim=' and 'ylim='. In your case, you would do: > plotDensities(yourobject, xlim=c(-10,30)) I would be concerned about getting such apparently HUGE numbers in some cases after your normalization - especially because the default for plotDensities is to plot R & G values in log2 scale! The extreme negative numbers in log2 are caused by very small positive numbers, but on the other end you shouldn't be getting anything close to 10000, or even 50 for that matter. It's probably only a few spots that are behaving strangely after the normalizations, but you might want to have a closer look at them. Cheers, Jenny At 08:17 AM 7/26/2006, Pete wrote: >Hi, >I'm still fairly new to all this so this may be a simple question. I have a >problem sometimes when using the plotDensities function in Limma, in some >cases the plot produced is on such a scale that the lines are not >distinguishable. Usually the intensity axis is in the range of -10 :30, >however ocassionally after a printtip lowes normalisation, or some >betweenArrayNormalizations, the scale of the graph is -5000:10000 with the >density peak being a single spike in the middle of the plot. Is there a way >to control the axis scale? or is there an easy way to set a minimum and >maximums for an MA object? > > >Many thanks > >Pete > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu