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

[Seth Falcon]

On 31 Aug 2005, pospisil at zbh.uni-hamburg.de wrote:
> 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

> 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

You might try traceback() just after the error occurs.  Folks on the
list will also need a bit more info to help you: R version, and
versions of the package(s) you are using.  The output of
session.info() is usually a great start.

Best,

+ seth