[BioC] R.fold and stdev in SAM (siggenes package)

Xia Han 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?



More information about the Bioconductor mailing list