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

[Stefano Calza]

Uh... how can it be a paired test if you don't have 2 measures for each unit?

In my humble opinion I wouldn't use a permutation test with such a small sample size, as your simulated null distribution would be quite coarse.

But witn a 2 vs 2, which actually is a n=2 sample size (being paired) I don't think you can do that much statistics.

HIH,
Stefano

On Fri, Apr 22, 2005 at 03:23:25PM +0000, Ken Termiso wrote:
<Ken>Hi all,
<Ken>
<Ken>I'm trying to do a paired 3control vs. 2experimental chip analysis with 
<Ken>SAM, and my class label is :
<Ken>
<Ken>sam.cl <- c(-3, -2, -1, 1, 2)
<Ken>
<Ken>but this throws an error :
<Ken>
<Ken>Error in adjust.for.mt(data, cl, var.equal = var.equal) :
<Ken>       Negative values are only allowed for the paired analysis. Or,
<Ken>if a paired analysis should be done: There is something wrong with the 
<Ken>class labels.
<Ken>
<Ken>
<Ken>So what should I do? Is it best to just drop one of the control chips so 
<Ken>that I have an equal number of control and experimental chips??? (It was 
<Ken>planned as a 3x3 comparison, but our core botched one of my experiemental 
<Ken>chips).
<Ken>
<Ken>Thanks,
<Ken>Ken
<Ken>
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