Dear List, I am using heatmap to output a microarray image to a pdf file. I get an error message when I do this: Error: PDF file is damaged - attempting to reconstruct xref table... Error: Couldn't find trailer dictionary Error: Couldn't read xref table The file opens fine in default mode "X11 I think". 1) Do people generally output to pdfs? 2) Is there a fix? If not what other formats to people output their graphics to in order to present them? TIA [[alternative HTML version deleted]]

Hi Pete: It is difficult for others to know what the problem is unless you send some code that would reproduce the error. For example, the following three lines would create a pdf document (in the working directory) with the image of a plot. > pdf(file="temp.pdf") > plot(1:10) > dev.off() I have checked; the file opens outside of R with the expected image. You can check if you are able to run this code and create a plot. If not, send all of the following: 1. the code 2. the R outputs and 3. output of the command sessionInfo() [look at an example below] Best, Saroj > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base ----- Original Message ----- From: "Pete Shepard" <peter.shepard@gmail.com> To: bioconductor at stat.math.ethz.ch Sent: Wednesday, March 11, 2009 5:30:25 PM GMT -05:00 US/Canada Eastern Subject: [BioC] heatmap output problems in pdf Dear List, I am using heatmap to output a microarray image to a pdf file. I get an error message when I do this: Error: PDF file is damaged - attempting to reconstruct xref table... Error: Couldn't find trailer dictionary Error: Couldn't read xref table The file opens fine in default mode "X11 I think". 1) Do people generally output to pdfs? 2) Is there a fix? If not what other formats to people output their graphics to in order to present them? TIA [[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 -- Computational Biology VBI @ Virginia Tech