[BioC] siggenes problem with paired observations

Patel, Anand Patel_A at kids.wustl.edu
Wed Nov 3 22:57:51 CET 2004


I'm trying to use sam to analyze 9 pairs of triplicate conditions, a subset of an exprSet.
It takes the subset just fine, but when I feed it the following vector as cl:
 
> cl
 [1] -1 -1 -1  1  1  1 -2 -2 -2  2  2  2 -3 -3 -3  3  3  3 -4 -4 -4  4  4  4  5  5  5  6  6  6 -5 -5 -5 -6 -6 -6 -7 -7 -7  7  7  7 -8 -8 -8  8  8  8 -9 -9 -9  9  9  9

> sam.out3 <- sam(subeset, cl)
Error in adjust.for.mt(data, cl, var.equal = var.equal) : 
        There is something wrong with the class labels.

If I change cl to make it 18 unrelated groups, it works, but they're not paired observations.
 
How can I get it to take these as pairs of observations?
 
Thanks,
Anand C. Patel, MD
Fellow, Pediatric Pulmonology
St. Louis Children's Hospital
 

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