Dear All
I am using the pamr.cv function from library pamr to cross-validate the
nearest shrunken centroid classifier. Th following command is being used:

NSC.results =pamr.cv(fit = NSC.trained, data = data)

The output  contains cols. containing the threshold values, no of genes and
the total errors.
The optimal threshold is chosen to be  the  threshold giving the minimum
error rate.
The command used for this is as follows:

optthresh <- NSC.results$threshold[minindex]

pamr.listgenes(NSC.trained, data, threshold=optthresh, genenames=TRUE)

However, if the total number of genes at the opt. threshold is only one the
following error mssg. is obtained:

Error in dimnames(res) <- list(NULL, c("id", gnhdr, schdr)) :

I have tried this with several data sets and the error persists. Hence, is
this an error in the code
or is PAM not supposed to work in case of a single gene surviving the
optimal threshold.


Thanks in advance!

ALok
-- 
Ph.D scholar
Centre of Computational Biology and Bioinformatics
School of Information Technology
JNU New Delhi

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