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

[Heike Pospisil]

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