[BioC] [SAM] Error in mat.sig[, "d.value"] : incorrect number of dimensions

[Holger Schwender]

Hi,

yes, exactly this is the problem. But this bug has been fixed in siggenes
1.2.17, the Release 1.6 version of Bioconductor.

Best,
Holger


> --- Ursprüngliche Nachricht ---
> Von: "Sabrina Carpentier" <sabrina.carpentier at curie.fr>
> An: "Heike Pospisil" <pospisil at zbh.uni-hamburg.de>,
> <bioconductor at stat.math.ethz.ch>
> Betreff: Re: [BioC] [SAM] Error in mat.sig[,	"d.value"] : incorrect number
> of dimensions
> Datum: Wed, 31 Aug 2005 16:39:07 +0200
> 
> Dear Heike,
> 
> I believe that there is a problem only because you have only one
> significant
> gene so that the mat.sig isn't anymore a matrix but a vector.
> 
> I already have the problem...
> 
> Hope that helps you
> 
> Sabrina
> 
> Sabrina Carpentier
> Service Bioinformatique
> Institut Curie - Bat. Trouillet Rossignol (4e étage)
> 26 rue d'Ulm - 75248 Paris Cedex 5 - FRANCE
> Tel : +33 1 42 34 65 21
> ----- Original Message ----- 
> From: "Heike Pospisil" <pospisil at zbh.uni-hamburg.de>
> To: <bioconductor at stat.math.ethz.ch>
> Sent: Wednesday, August 31, 2005 10:10 AM
> Subject: [BioC] [SAM] Error in mat.sig[,"d.value"] : incorrect number of
> dimensions
> 
> 
> > Hello List,
> >
> > I have a problem performing SAM-analysis.
> >
> > I have 78 array, 47 of them have to be analysed:
> >  > dim(exprs(data)[,which(cl==1 | cl==0)])
> > [1] 54675    47
> >
> >
> > Vector cl contains the groups for all 78 chips, cl_0 only for those
> being
> of
> > interest:
> >  > cl
> >   [1]  1  1  1  1 NA  1  1  0  0  0  1  1 NA  1 NA NA  0  1  0 NA  0  1
> NA
> 1  1
> > [26] NA NA  1 NA NA  1 NA  0 NA  1  1 NA NA NA NA NA NA  0  1 NA  0  0
> NA
> 0  0
> > [51]  0  0 NA NA  1 NA  0 NA NA NA NA NA  1 NA  0  0  0 NA  0  0 NA  0 
> 1
> 0  0
> > [76]  0  0  0
> >  > cl_0
> >   [1] 1 1 1 1 1 1 0 0 0 1 1 1 0 1 0 0 1 1 1 1 1 0 1 1 0 1 0 0 0 0 0 0 1
> 0
> 1 0 0 0
> > [39] 0 0 0 1 0 0 0 0 0
> >
> > SAM works without any problem:
> > sam.out<-sam(exprs(data)[,which(cl==1 | cl==0)],cl_0,rand=123)
> >
> > It is possible to plot the result with plot(sam.out,0.5), but the
> summary
> > function results in an error message:
> >  > sum.sam.out<-summary(sam.out,0.5,ll=FALSE)
> > SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances
> >
> > s0 = 0.0122  (The 0 % quantile of the s values.)
> >
> >   Number of permutations: 100
> >
> >   MEAN number of falsely called genes is computed.
> >
> >   Delta: 0.5
> >   cutlow: -Inf
> >   cutup: 4.25703
> >   p0: 1
> >   Significant Genes: 1
> >   Falsely Called Genes: 0.19
> >   FDR: 0.19
> >
> >
> > Error in mat.sig[, "d.value"] : incorrect number of dimensions
> >
> > The length of vector cl_0 equals to the columns of
> exprs(data)[,which(cl==1 |
> > cl==0)].
> > Do you have any idea? Thanks a lot in advance,
> > Heike
> > -- 
> > Dr. Heike Pospisil
> > Center for Bioinformatics, University of Hamburg
> > Bundesstrasse 43, 20146 Hamburg, Germany
> > phone: +49-40-42838-7303 fax: +49-40-42838-7312
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> 
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