[BioC] Siggenes SAM analysis with unequal # of control and exp chips

[Ken Termiso]

Hi all,

I'm trying to do a paired 3control vs. 2experimental chip analysis with SAM, 
and my class label is :

sam.cl <- c(-3, -2, -1, 1, 2)

but this throws an error :

Error in adjust.for.mt(data, cl, var.equal = var.equal) :
        Negative values are only allowed for the paired analysis. Or,
if a paired analysis should be done: There is something wrong with the class 
labels.


So what should I do? Is it best to just drop one of the control chips so 
that I have an equal number of control and experimental chips??? (It was 
planned as a 3x3 comparison, but our core botched one of my experiemental 
chips).

Thanks,
Ken