For this, you could correlate the expression profile of your gene of interest against all the others on your chip and then plot the profiles in form of a line graph. Here is a short example using some random data: ## (1) Correlation Search x <- data.frame(y1=rnorm(10),y2=rnorm(10),y3=rnorm(10),y4=rnorm(10)) rownames(x) <- month.name[1:10] # correlation analysis gene "August" against all others y <- data.frame(apply(as.matrix(x), 1, cor, as.vector(as.matrix(x["August",])), method="pearson")) names(y)[1] <- c("PearsonCC") # Combine data and sort by correlation coefficient y <- cbind(x, y) y[order(-y[,5]), ] ## (2) Plot Top Five Hits in Form of a Line Graph y <- t(y[1:5,1:4]) plot(y[,1], type="l", lwd=2, col="blue") # Plots a line graph split.screen(c(1,1)) plot(y[,1], ylim=c(0,1), xlab="Measurement", ylab="Intensity", type="l", lwd=2, col=1) for(i in 2:length(y[1,])) { screen(1, new=FALSE) plot(y[,i], type="l", lwd=2, col=i, xaxt="n", yaxt="n", ylab="", xlab="", main="", bty="n") } close.screen(all=TRUE) # Pl On Mon 01/14/08 09:33, Lana Schaffer wrote: > Jim, > I am just asking about the expression of a single gene across all the > samples. > I have been reminded that genefinder would be a for me and I have used > it before. > Thanks, > Lana > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Monday, January 14, 2008 9:25 AM > To: Lana Schaffer > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] matching expression profiles > > Hi Lana, > > What exactly do you mean by 'expression profiles'? > > If you mean e.g., person A says these 100 genes are interesting in the > experimental system I am investigating, and I want to compare my results > to hers, then I think you want to use GSEA. > > I am most familiar with the variant in the Category package, but you > might also consider PGSEA or GSEAbase, depending on where your > expression profile comes from. > > Best, > > Jim > > > > Lana Schaffer wrote: > > Friends, > > What packages would you recommend in Bioconductor that would match > > expression profiles similar to a given expression profile and perhaps > > draw them ? > > Thanks, > > Lana Schaffer > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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 > -- Thomas Girke Assistant Professor of Bioinformatics Director, IIGB Bioinformatic Facility Center for Plant Cell Biology (CEPCEB) Institute for Integrative Genome Biology (IIGB) Department of Botany and Plant Sciences 1008 Noel T. Keen Hall University of California Riverside, CA 92521 E-mail: thomas.girke at ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-827-2469 Fax: 951-827-4437