I am using the plotAffyRNAdeg function from affy to create a RNA digestion plot. I use the following code Data <- ReadAffy() deg<-AffyRNAdeg(Data[,c(1,2,3,4)]) jpeg(file="RNA_digestion_plot.jpeg") plotAffyRNAdeg(deg,col=c(1,2,3,4)) labels<-c("E2h rep 1", "E2h rep 2", "E2h rep 3", "E2h rep 4") legend(5,6,labels,lty=1,col=c(1,2,3,4)) dev.off() The problem I have is that the x-axis is too short (only extends 0-10) and the lines extend over the end. How do I extend the x-axis up to 15 as I have 13 probes? Thanks Sue Jones

Hi Sue, Sue Jones wrote: > > I am using the plotAffyRNAdeg function from affy to create a RNA digestion > plot. I use the following code > > Data <- ReadAffy() > deg<-AffyRNAdeg(Data[,c(1,2,3,4)]) > jpeg(file="RNA_digestion_plot.jpeg") > plotAffyRNAdeg(deg,col=c(1,2,3,4)) > labels<-c("E2h rep 1", "E2h rep 2", "E2h rep 3", "E2h rep 4") > legend(5,6,labels,lty=1,col=c(1,2,3,4)) > dev.off() > > The problem I have is that the x-axis is too short (only extends 0-10) > and the lines extend over the end. How do I extend the x-axis up to 15 as > I have 13 probes? The xlim argument is automatically set in the plotAffyRNAdeg() function, so you won't be able to extend it without doing some hacking. You can either copy and paste the function into an editor, change it to your liking and then source() it back in, or if you can install source packages, you can change the source .R file and then re-build the package. Of course this is a bit of work to just make this slight change. You might also want to add width = 700, height = 700 (or something similar) to your call to jpeg(), which will make the resulting plot a reasonable size. Best, Jim > > > Thanks > > Sue Jones > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hi Sue, Please don't respond only to me. I may actually say something brilliant one day, and would like it saved for posterity on the archives of the listserv ;-D. Seriously though, you should always keep responses on the list so people can (possibly) find answers to their questions. Sue Jones wrote: > > Hi James > > Thanks for replying - if the x-axis is set automatically - how come > it comes up short in my case? I get the figure I attach ... Good question. You might try debug(plotAffyRNAdeg) plotAffyRNAdeg(deg) and step through the function to see what xlim values are being set. I have never seen a plot like the one you get (and actually don't know of an Affy chip with 14 probes per probeset), so am not sure why you are getting these results. > > Also I am slightly concerned that I do not have smoother lines on the > plot - > many I have seen in publications are straightish lines - should I just > be using PM data for this plot? By default you *are* using PM data. > > But I am right its not the slopes of the lines is the key but the fact that > the shapes should all be similar across the arrays? I have never been bothered by the shape of these plots - the only thing I look for is consistent slopes between the samples. Averaging the PM probes based on their position in the probeset (across all probesets) is not biologically sensical, so I don't think the shape of the lines has any meaning. It's just a way to estimate the degradation of mRNA, and possibly the quality of the IVT step. Best, Jim > > Many thanks for your time. > > Sue > > > On Wed, 14 Jun 2006, James W. MacDonald wrote: > >> Hi Sue, >> >> Sue Jones wrote: >> >>> >>> I am using the plotAffyRNAdeg function from affy to create a RNA >>> digestion plot. I use the following code >>> >>> Data <- ReadAffy() >>> deg<-AffyRNAdeg(Data[,c(1,2,3,4)]) >>> jpeg(file="RNA_digestion_plot.jpeg") >>> plotAffyRNAdeg(deg,col=c(1,2,3,4)) >>> labels<-c("E2h rep 1", "E2h rep 2", "E2h rep 3", "E2h rep 4") >>> legend(5,6,labels,lty=1,col=c(1,2,3,4)) >>> dev.off() >>> >>> The problem I have is that the x-axis is too short (only extends >>> 0-10) and the lines extend over the end. How do I extend the x-axis >>> up to 15 as I have 13 probes? >> >> >> The xlim argument is automatically set in the plotAffyRNAdeg() >> function, so you won't be able to extend it without doing some >> hacking. You can either copy and paste the function into an editor, >> change it to your liking and then source() it back in, or if you can >> install source packages, you can change the source .R file and then >> re-build the package. >> >> Of course this is a bit of work to just make this slight change. >> >> You might also want to add width = 700, height = 700 (or something >> similar) to your call to jpeg(), which will make the resulting plot a >> reasonable size. >> >> Best, >> >> Jim >> >>> >>> >>> Thanks >>> >>> Sue Jones >>> >>> _______________________________________________ >>> 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 >> >> >> >> -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.