[BioC] Problem loading files into limmaGUI

Gordon Smyth smyth at wehi.edu.au
Fri Jun 25 10:43:05 CEST 2004

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.


At 05:12 PM 25/06/2004, Peter Baker (CMIS, St Lucia) wrote:
>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
>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 at csiro.au>
>WWW: http://www.cmis.csiro.au/Peter.Baker/
>Phone:+61 7 3214 2210   Fax:+61 7 3214 2900

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