Hi, I'm trying to make pdf for mfuzzPlot (please see script below), but I keep getting an error saying the file is not recognizable or corrupted (please see attachment). The mfuzzPlot can be displayed in R but not written as a PDF?! ---------------------- mfuzzPlot <- mfuzz.plot(eset.s, cl = cl, mfrow = c(4,4), time.labels = c(0,1,2,5,10,15,30,60) ) pdf(file = paste("MfuzzPlot", sample_output, ct, mb, ".pdf", sep="_")) mfuzzPlot dev.off() --- or pdf(file = paste("MfuzzPlot", sample_output, ct, mb, ".pdf", sep="_")) mfuzzPlot <- mfuzz.plot(eset.s, cl = cl, mfrow = c(4,4), time.labels = c(0,1,2,5,10,15,30,60) ) dev.off() ___________ I'd very much appreciate your feedback. Thanks, Dorothy

Hi Dorothy, dorothyc wrote: > Hi, > > I'm trying to make pdf for mfuzzPlot (please see script below), but I > keep getting an error saying the file is not recognizable or corrupted > (please see attachment). The mfuzzPlot can be displayed in R but not > written as a PDF?! The plot can be written to a pdf, but you have to override some of the defaults, namely the insistence that plots appear in new windows. The following works for me (using the examples for mfuzz.plot): > data(yeast) > yeastF <- filter.NA(yeast) 49 genes excluded. > yeastF <- fill.NA(yeastF) > yeastF <- standardise(yeastF) > cl <- mfuzz(yeastF,c=20,m=1.25) > pdf("Mfuzz.pdf") > mfuzz.plot(yeastF, cl, c(2,2), new.window = FALSE) > dev.off() windows 2 Try that and see if it works for you. Best, Jim > > ---------------------- > mfuzzPlot <- mfuzz.plot(eset.s, cl = cl, mfrow = c(4,4), time.labels = > c(0,1,2,5,10,15,30,60) ) > pdf(file = paste("MfuzzPlot", sample_output, ct, mb, ".pdf", sep="_")) > mfuzzPlot > dev.off() > --- or > pdf(file = paste("MfuzzPlot", sample_output, ct, mb, ".pdf", sep="_")) > mfuzzPlot <- mfuzz.plot(eset.s, cl = cl, mfrow = c(4,4), time.labels = > c(0,1,2,5,10,15,30,60) ) > dev.off() > ___________ > > I'd very much appreciate your feedback. > > Thanks, > Dorothy > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826