[BioC] R.fold and stdev in SAM (siggenes package)
xia.han at bms.com
Fri Jun 3 16:42:38 CEST 2005
I have a 2 class data, and am trying to get the output from sam in
siggenes package using these commands:
sam.data <- sam(data, cl, rand=123, B=1000)
sam.out.data <- summary(sam.data, 1.9)$mat.sig
In the output, q.value and p.value look ok, but many R.fold are "Inf" or
0, which don't make sense. Also the stdev results are much smaller than
what I get using sd( ). Can anyone help me on this?
Also, Is there anyway I could get the matrix from mat.sig for the whole
data instead of a subset difined by specific delta value?
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