[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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