Took a few days, but I'm up to speed with R and Bioconductor. I have the individual plots working via X11, but the diagnostic plots are causing me trouble. I'm having a problem that I saw (in the mailing list archives) was related to the layout subroutine. When I run the diagnostic plots, I get the following errors: > maNormPlots(name.norm[,1],save=TRUE,fname="maNorm_Plots.ps",dev="posts cr ipt") Error in plot.new() : Figure margins too large > maRawPlots(name.raw[,1],save=TRUE,fname="maRaw_Plots.ps",dev="postscri pt ") Error in factor(z, levels = 1:nlevels(x), labels = levels(x), ordered = is.ordered(x)) : invalid labels; length 0 should be 1 or 2 Has this bug been investigated or is there a workaround? Can anyone offer help? Thanks. My details: (Mac OS X 10.2.6, BioC 1.2, R 1.7.1, iBook 600mHz, 640MB RAM) > version _ platform powerpc-apple-darwin6.6 arch powerpc os darwin6.6 system powerpc, darwin6.6 status major 1 minor 7.1 year 2003 month 06 day 16 language R

Hi Mike Possibly not that much help, but I have encountered the "Figure margins too large" problem before, and it is what it says it is - basically something is trying to fit a graph or figure into an image (postscript in your case) that isn't big enough. Somewhere, the code is setting the size of the postscript image output to be a certain size and your graph is bigger. I don't know maNormPlots() very well, but check the documentation to see if somehow you can play about with the image output size Cheers Mick -----Original Message----- From: Mike Schaffer [mailto:mschaff@bu.edu] Sent: 01 September 2003 07:16 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Diagnostic plots error Took a few days, but I'm up to speed with R and Bioconductor. I have the individual plots working via X11, but the diagnostic plots are causing me trouble. I'm having a problem that I saw (in the mailing list archives) was related to the layout subroutine. When I run the diagnostic plots, I get the following errors: > maNormPlots(name.norm[,1],save=TRUE,fname="maNorm_Plots.ps",dev="posts cr ipt") Error in plot.new() : Figure margins too large > maRawPlots(name.raw[,1],save=TRUE,fname="maRaw_Plots.ps",dev="postscri pt ") Error in factor(z, levels = 1:nlevels(x), labels = levels(x), ordered = is.ordered(x)) : invalid labels; length 0 should be 1 or 2 Has this bug been investigated or is there a workaround? Can anyone offer help? Thanks. My details: (Mac OS X 10.2.6, BioC 1.2, R 1.7.1, iBook 600mHz, 640MB RAM) > version _ platform powerpc-apple-darwin6.6 arch powerpc os darwin6.6 system powerpc, darwin6.6 status major 1 minor 7.1 year 2003 month 06 day 16 language R _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor