Hi Seby, On Wed, 23 Jun 2004, Seby wrote: > I am using LimmaGUI for a micro array data analysis..Is there anyway I can > export the M values for all genes along with the gene names...right now It > exports M values but doesnt have the gene names or ID columns.. I've just uploaded a new version of limmaGUI (1.1.4) to: http://bioinf.wehi.edu.au/limmaGUI/ which has this feature you have requested. You can install it with: install.packages("limmaGUI",contriburl="http://bioinf.wehi.edu.au/limm aGUI") after checking that .libPaths() gives an appropriate R library directory for installation. limmaGUI now includes all columns from the GAL file when it exports M values or A values, and while the format is still the same (tab-delimited text), the default file extension is now ".xls", so that you can double-click on the file and it will open up automatically in Excel. (The ".xls" extension for tab-delimited text is also used in other places, e.g. the Stanford Microarray Database.) Also, "Export M" and "Export A" now appear in the "File" menu, just above "Export HTML Report". They will eventually be removed from the "Normalization" menu. I'll do something similar for affylmGUI soon. Another thing on my "TO DO" list for limmaGUI is to make the GAL file optional like it is in limma. It makes sense to require a GAL file for "Spot" image analysis files which is what I started out using, but it shouldn't be required for other formats like "ImaGene". Regards, James

Hi, On Thu, 24 Jun 2004, James Wettenhall wrote: > I'll do something similar for affylmGUI soon. This is done now in affylmGUI 1.1.4, available from: http://bioinf.wehi.edu.au/affylmGUI/ http://bioinf.wehi.edu.au/affylmGUI/affylmGUI_1.1.4.tar.gz http://bioinf.wehi.edu.au/affylmGUI/affylmGUI_1.1.4.zip Should appear on BioC devel soon. Regards, James affylmGUI 1.1.4 Changes ----------------------- - Export Normalized Expression Values has been added to the File menu and will eventually be removed from the Normalization menu. - The probe-set-IDs were already included when exporting expression data from affylmGUI, so there was no need to add extra column(s) as was done in the recent limmaGUI update. - Now when tab-delimited text files are exported from affylmGUI (normalized expression values), the default extension is ".xls", so that you can double-click to open them in Excel. - Handling of temporary files has been cleaned up a bit. If using the advanced "Evaluate R code" functionality, which evaluates R code within affylmGUIenvironment, (the environment containing the current microarray data set), any temporary files required are now saved to tempfile() rather than to the current working directory.