[BioC] "limma" and "Imagene"

Gordon Smyth smyth at wehi.edu.au
Thu Jul 1 23:45:15 CEST 2004

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.


At 08:23 PM 1/07/2004, Breuk102 wrote:
>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 ?
>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 at bio.uu.nl
>website: http://genomics.bio.uu.nl/

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