Hi We have affylmGUI running on Mac OSX and R2 dev. A couple of things seem not to work. We can save all the plots except for venn diagrams where we get an error message saying: Error in paste(limmaDataSetNmaeText, "VennDiagram", sep = "") : Object "limmaDataSetNameText" not found When we try to do a Heat diagram we get this error message: Error in try(expr, TRUE): No loop to break from, jumping to top level followed by a second error message: Cannot find package drosgenome1 (ours are Drosophila chips and the drosgenome1 package is installed in /users/me/Library/R/library/drosgenome1cdf) There are then a bunch of related messages to not finding drosgenome1 In the end we end up with a black heat diagram. Perhaps, related to this when we try to use gene symbols instead of probe ids we get this error message: Error in "[.data.frame"(genelist, topGenes, IDorSymbol) : undefined columns selected What P value is used to define significant in the venn diagram? thanks, Simon

Simon, As we are leading up to a Release version of 1.4, I'll just explain what needs to be fixed in affylmGUI and check with Jeff that's it OK to fix these things, rather than rushing in and changing things... > We have affylmGUI running on Mac OSX and R2 dev. A couple of things Great! > seem not to work. We can save all the plots except for venn diagrams > Object "limmaDataSetNameText" not found This bug is easy to fix. Should be able to insert this patch for the 1.4 release. The following line needs to be inserted at the beginning of the VennDiagramPlot function in affylmGUI's plot.R : Try(limmaDataSetNameText <- get("limmaDataSetNameText",envir=affylmGUIenvironment)) [Don't get too confused by the Try(...). That's just affylmGUI's way of diverting error messages to messageBoxes] > Error in try(expr, TRUE): No loop to break from, jumping to top level This appears to be an incorrect use of break() in the HeatDiagramPlot function in affylmGUI's plot.R. The incorrect code is : Try(if is.na(matchIndex)) break()) [ More code within large if-block ] It should be: Try(if (!is.na(matchIndex)) { [ More code within large if-block ] }) > Cannot find package drosgenome1 At the moment, some affylmGUI functions will complain if there is no annotation package available for your chip. Usually this is just a harmless but annoying message box, on which you can click "OK". You may have to put up with this annoying behaviour for the 1.4 Release, but there are some related bugs which you encountered around the same time as this annoying "warning". The following lines of code in the HeatDiagramPlot function in affylmGUI's plot.R will fail if there is no annotation package, i.e. they are incorrect: Try(genelist <- cbind(as.matrix(ls(cdfenv)),as.matrix(geneSymbols))) ... Try(heatdiagram(abs(eb$t),fit$coefficients,primary=1, critical.primary=primaryCutoff,critical.other=otherCutoff, names=substr(geneSymbols,1,20),main=plotTitle)) The first line of code above can be deleted ("genelist" is not used in PlotHeatDiagram) and replaced with: Try(if (length(geneSymbols)>0) geneLabels <- geneSymbols else geneLabels <- ls(cdfenv)) and the second can be modified by replacing "geneSymbols" by "geneLabels" : Try(heatdiagram(abs(eb$t),fit$coefficients,primary=1, critical.primary=primaryCutoff,critical.other=otherCutoff, names=substr(geneLabels,1,20),main=plotTitle)) > What P value is used to define significant in the venn diagram? OK, this probably should become part of a dialog box, but I don't think it will happen before the 1.4 Release. The venn diagram plotting function calls limma's classifyTestsF which seems to have a default p-value of 0.01 : library(limma) ?classifyTestsF You might get more discussion about that by posting with a different subject-line like "limma classifyTestsF p-value" Regards, James ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au

Simon, On Tue, 11 May 2004, Simon Kidd wrote: > I got error messages when I tried to make these changes in affylmGUI > so I think I will wait for the new release version. The affylmGUI patches have been committed to Bioconductor, but they may take a while to show up. I have tested them with a malaria data set with no annotation package, and the main problems you encountered appear to be fixed. You should be able to see the changes straight away at : http://bioinf.wehi.edu.au/affylmGUI/ You can obtain them with: install.packages("affylmGUI", contriburl="http://bioinf.wehi.edu.au/affylmGUI") I have modified the DESCRIPTION file, so that the version number is increased to 0.4.6 and the date is changed to May 12. If you tried modifying affylmGUI yourself, you should not expect to be able to modify the R code directly in $R_DIRECTORY\library\affylmGUI\R\ Instead you could unzip the source (.tar.gz) package OUTSIDE the $R_DIRECTORY\library tree with : tar zxvf then modify the R code then use R CMD build affylmGUI (to build a new .tar.gz source package) then R CMD INSTALL affylmGUI_0.4.6.tar.gz (to install affylmGUI from source) Or if you want a binary, e.g. on Windows, you can use: Rcmd build --binary affylmGUI Regards, James