Hello, I am a recent user of the limmaGUI package. I am having trouble loading in GenePix files into the most recent version of limmaGUI (v1.1.3). At first I had no problem. I downloaded the .exe file that installed limma v1.6.10 and limmaGUI v1.0.2. Then I uploaded 4 GenePix files, a GAL file, RNA targets file and Spot Types file. Everything was fine. I could make plots and do the linear modeling. But, when I just recently updated the limma and limmaGUI packages to v1.6.14 and v1.1.3, respectively, I could no longer load the files that worked fine in the older version. I would get the error "Reading image processing files failed: unable to read imaging processing file." So the RG object wouldn't get created and nothing was loaded. I tried saving the files under new names and trying again. I checked that everything was tab-delimited text. No luck. I also tested the files by loading them using the older version of limmaGUI (v1.0.2) and they loaded no problem. So the files themselves must be fine. It's really quite strange. Has anyone had a problem similar to this? Any suggestions? Thanks, ED -- Elva Diaz, Ph.D. Assistant Professor University of California at Davis Med-Pharmacology & Toxicology 1339 Tupper Hall Davis, CA 95616 (530) 754-6080 office (530) 752-7710 fax ediaz@ucdavis.edu http://som.ucdavis.edu/departments/pharmacology/departmentlabs/elvadia z/diaz lab/index_html

ED I had the same problem (well I use limma rather than limmaGUI) so I just downgraded back to the versions on Bioconductor and everything works fine again It gave some slpitstring error when reading genepix file(s) but I've forgotten the exact details Cheers Peter On Wed, 23 Jun 2004, Elva Diaz wrote: >Hello, > >I am a recent user of the limmaGUI package. I am having trouble loading in >GenePix files into the most recent version of limmaGUI (v1.1.3). > >At first I had no problem. I downloaded the .exe file that installed limma >v1.6.10 and limmaGUI v1.0.2. Then I uploaded 4 GenePix files, a GAL file, >RNA targets file and Spot Types file. Everything was fine. I could make >plots and do the linear modeling. > >But, when I just recently updated the limma and limmaGUI packages to v1.6.14 >and v1.1.3, respectively, I could no longer load the files that worked fine >in the older version. I would get the error "Reading image processing files >failed: unable to read imaging processing file." So the RG object wouldn't >get created and nothing was loaded. > >I tried saving the files under new names and trying again. I checked that >everything was tab-delimited text. No luck. I also tested the files by >loading them using the older version of limmaGUI (v1.0.2) and they loaded no >problem. So the files themselves must be fine. It's really quite strange. > >Has anyone had a problem similar to this? Any suggestions? > >Thanks, >ED > -- Dr Peter Baker, Statistician (Bioinformatics/Genetics), CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct 306 Carmody Road, St Lucia Qld 4067. Australia. Email: <peter.baker@csiro.au> WWW: http://www.cmis.csiro.au/Peter.Baker/ Phone:+61 7 3214 2210 Fax:+61 7 3214 2900

The bug is caused by readGPRHeader() in limma assuming that certain entries are in the genepix header section. I have fixed the bug and it will be in limma 1.7.0 in a few days. The use of readGPRHeader() was introduced in limma 1.6.12 to solve a problem previously seen where different gpr files have different numbers of header records. Gordon At 05:12 PM 25/06/2004, Peter Baker (CMIS, St Lucia) wrote: >ED > >I had the same problem (well I use limma rather than limmaGUI) so I >just downgraded back to the versions on Bioconductor and everything >works fine again > >It gave some slpitstring error when reading genepix file(s) but I've >forgotten the exact details > >Cheers >Peter > > >On Wed, 23 Jun 2004, Elva Diaz wrote: > > >Hello, > > > >I am a recent user of the limmaGUI package. I am having trouble loading in > >GenePix files into the most recent version of limmaGUI (v1.1.3). > > > >At first I had no problem. I downloaded the .exe file that installed limma > >v1.6.10 and limmaGUI v1.0.2. Then I uploaded 4 GenePix files, a GAL file, > >RNA targets file and Spot Types file. Everything was fine. I could make > >plots and do the linear modeling. > > > >But, when I just recently updated the limma and limmaGUI packages to v1.6.14 > >and v1.1.3, respectively, I could no longer load the files that worked fine > >in the older version. I would get the error "Reading image processing files > >failed: unable to read imaging processing file." So the RG object wouldn't > >get created and nothing was loaded. > > > >I tried saving the files under new names and trying again. I checked that > >everything was tab-delimited text. No luck. I also tested the files by > >loading them using the older version of limmaGUI (v1.0.2) and they loaded no > >problem. So the files themselves must be fine. It's really quite strange. > > > >Has anyone had a problem similar to this? Any suggestions? > > > >Thanks, > >ED > > > > >-- >Dr Peter Baker, Statistician (Bioinformatics/Genetics), >CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct >306 Carmody Road, St Lucia Qld 4067. Australia. >Email: <peter.baker@csiro.au> >WWW: http://www.cmis.csiro.au/Peter.Baker/ >Phone:+61 7 3214 2210 Fax:+61 7 3214 2900