[BioC] Problems using rMAT tutorial

[Wolfgang Huber]

Dear Patrick

the first thing you could do is upgrade your R and rMAT. I doubt anyone 
here is interested in debugging older versions. The last release version 
of rMAT was 2.3.4, you're using 1.1.2.

And btw a new release is imminent:
http://wiki.fhcrc.org/bioc/BioC_2.6_Release_Schedule

	Best wishes
	Wolfgang

  Schorderet ha scritto:
> Dear All,
> 
> I have been trying to use rMAT and its tutorial (http://wiki.rglab.org/index.php?title=Public:RMAT 
> ). I am working with MacOSX and a recent R version. I was able to  
> install rMAT (at least it loads correctly in R when launching it from  
> the package manager window) as well as the data set which is used in  
> the tutorial. I can load the different datasets separately, but when I  
> try to combine them into a single variable, I get this error message  
> (see below). I do not know what is going on.. R seems to be unable to  
> convert some variables (see error highlighted in red).
> 
> I would appreciate any help. Thanks in advance,
> 
> Patrick
> 
> 
> 
> R version 2.9.1 (2009-06-26)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> 
> R est un logiciel libre livré sans AUCUNE GARANTIE.
> Vous pouvez le redistribuer sous certaines conditions.
> Tapez 'license()' ou 'licence()' pour plus de détails.
> 
> R est un projet collaboratif avec de nombreux contributeurs.
> Tapez 'contributors()' pour plus d'information et
> 'citation()' pour la façon de le citer dans les publications.
> 
> Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
> en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
> Tapez 'q()' pour quitter R.
> 
> [R.app GUI 1.28 (5444) i386-apple-darwin8.11.1]
> 
> 
> 
> 
> Attachement du package : 'gsl'
> 
> 
> 	The following object(s) are masked from package:stats :
> 
> 	 sd
> 
> Le chargement a nécessité le package : biomaRt
> Le chargement a nécessité le package : grid
> 
> 
> celA<-c("MCF_ER_A1.CEL","MCF_ER_A3.CEL", "MCF_ER_A4.CEL",  
> "MCF_INP_A1.CEL", "MCF_INP_A3.CEL","MCF_INP_A4.CEL")
>  > ERA<-BPMAPCelParser(bpmapA, celA, seqName="chr2")
>  > bpmapB<-"P1_CHIP_B.Anti-Sense.hs.NCBIv35.NR.bpmap"
>  > celB<-c("MCF_ER_B1.CEL","MCF_ER_B3.CEL", "MCF_ER_B4.CEL",  
> "MCF_INP_B1.CEL", "MCF_INP_B3.CEL","MCF_INP_B4.CEL")
>  > ERB<-BPMAPCelParser(bpmapB, celB, seqName="chr2")
>  > bpmapC<-"P1_CHIP_C.Anti-Sense.hs.NCBIv35.NR.bpmap"
>  > celC<-c("MCF_ER_C1.CEL","MCF_ER_C3.CEL", "MCF_ER_C4.CEL",  
> "MCF_INP_C1.CEL", "MCF_INP_C3.CEL","MCF_INP_C4.CEL")
>  > ERC<-BPMAPCelParser(bpmapC, celC, seqName="chr2")
> 
> 
> Erreur dans .Method(..., deparse.level = deparse.level) :
>    pas de méthode pour convertir automatiquement cette classe S4 en  
> vecteur
> 
> 
>  > sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-apple-darwin8.11.1
> 
> locale:
> fr_CH.UTF-8/fr_CH.UTF-8/C/C/fr_CH.UTF-8/fr_CH.UTF-8
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets   
> methods   base
> 
> other attached packages:
> [1] GenomeGraphs_1.4.1 biomaRt_2.0.0      gsl_1.8-14         rMAT_1.1.2
> 
> loaded via a namespace (and not attached):
> [1] affxparser_1.16.0 Biobase_2.4.1     RCurl_0.98-1      XML_2.6-0
> 
>   
>   
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber