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Heike Pospisil
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310
@heike-pospisil-1097
Last seen 10.2 years ago
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