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

[Sabrina Carpentier]

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
>
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