Hi, I have found a problem with the limma, limmaGUI combination: (v 1.7.1 limma, and 1.2.1 GUI). The latest install was used (downloaded from the limmaGUI site) to install the newest R 1.9.1 and packages. After installing I tried to load my ImaGene 6.5.1 data into limmaGUI which didn't work. limmaGUI reported that is was unable to read the image processing files. I have used older versions off limma/limmaGUI before and this always worked. After trying several things (changing files, renaming and so on) I downgraded the limma package to version 1.6.6 and suddenly everything worked like before. Probably the newest limma package read the imagene files differently than the older versions ? Sadly this older version together with limmaGUI still requires a GAL file (newest option in GUI was that it can determine the slide layout automatically from the ImaGene file and so no GAL file is needed). Anybody else knows why the newest version of limma and limmaGUI don't work, or have this problem solved ? Yours, Bas ================================= Dr. Ir. B. van Breukelen PostDoc, Bioinformatics, Molecular genetics Dept. of Biology. Room N407: H.R. Kruytgebouw Padualaan 8 3574 CH Utrecht Tel: +31(0)30 253 3355 Mobile: +31(0)6 24 996046 e-mail: b.vanbreukelen@bio.uu.nl website: http://genomics.bio.uu.nl/ ================================= [[alternative HTML version deleted]]

Bas, It looks like you forget to mention the output on the R console when you try to read in your Imagene files (which you told me off the BioC list) : - The R_GUI reports: Read header information Warning message: Coercing LHS to a list - Loading and 'old' *.lma (.RData) files works ok. James

I managed to break the reading of imagene data into limma when I implemented some 'simplifications' of readImaGeneHeader() on June 8. It is now fixed in limma 1.7.2 available from http://bioinf.wehi.edu.au/limma. This should work fine with the latest limmaGUI. Gordon At 08:23 PM 1/07/2004, Breuk102 wrote: >Hi, > >I have found a problem with the limma, limmaGUI combination: (v 1.7.1 limma, >and 1.2.1 GUI). >The latest install was used (downloaded from the limmaGUI site) to install >the newest R 1.9.1 and packages. After >installing I tried to load my ImaGene 6.5.1 data into limmaGUI which didn't >work. limmaGUI reported that is was unable to read the >image processing files. I have used older versions off limma/limmaGUI before >and this always worked. After trying several >things (changing files, renaming and so on) I downgraded the limma package >to version 1.6.6 and suddenly everything worked like >before. Probably the newest limma package read the imagene files differently >than the older versions ? Sadly this older version together with >limmaGUI still requires a GAL file (newest option in GUI was that it can >determine the slide layout automatically from the ImaGene file and so no GAL > >file is needed). > >Anybody else knows why the newest version of limma and limmaGUI don't work, >or have this problem solved ? > >Yours, > >Bas >================================= >Dr. Ir. B. van Breukelen >PostDoc, Bioinformatics, Molecular genetics >Dept. of Biology. >Room N407: H.R. Kruytgebouw >Padualaan 8 >3574 CH Utrecht > >Tel: +31(0)30 253 3355 >Mobile: +31(0)6 24 996046 >e-mail: b.vanbreukelen@bio.uu.nl >website: http://genomics.bio.uu.nl/ >=================================