Dear Greg, This looks helpful, and easy to incorporate into the limma package. I'm currently travelling at some conferences. Will follow-up with you in a couple of weeks. At that time I'll also ask for a sample of a bluefuse output file. Gordon > Date: Wed, 06 Jul 2005 15:22:11 +0100 > From: Gregory Lefebvre <gl2 at="" sanger.ac.uk=""> > Subject: [BioC] bluefuse export and limma read.maimages > To: bioconductor at stat.math.ethz.ch > > Hi all, > > here are some hacks added to read.maimages() function in LIMMA package, > in order to read BlueFuse export files. > It works fine for me. > > Let me know. > Greg > (code deleted)

Dear Greg, Support for BlueFuse export files how now been added to limma 2.0.3, available from http://bioinf.wehi.edu.au/limma. Please try it out. There are some minor changes from your code: - BlueFuse doesn't provide background intensities, so only foreground intensities are read. The background columns are not set at all. This will work correctly with all limma functions which operate on RGList objects. - The gene annotation columns are left the same as in the export file, i.e., in capitals. - FLAG column is not read into the annotation data frame, because it is array-specific The function readBlueFuseHeader() now returns an error whenever the second line is not blank. Gordon > Date: Wed, 06 Jul 2005 15:22:11 +0100 > From: Gregory Lefebvre <gl2 at="" sanger.ac.uk=""> > Subject: [BioC] bluefuse export and limma read.maimages > To: bioconductor at stat.math.ethz.ch > > Hi all, > > here are some hacks added to read.maimages() function in LIMMA package, > in order to read BlueFuse export files. > It works fine for me. > > Let me know. > Greg > (code deleted)