[BioC] How to get all genes in the summary table of siggenes SAM

Wayne Xu wxu at msi.umn.edu
Mon Apr 28 22:15:17 CEST 2008


Hello,
Is there a way to get all genes' info in the SAM result table?

sam.out <- sam(samples.mat,cl,method="d.stat",rand=123,p0=0.95);
sum.table<-summary(sam.out,0,ll=F,file = "result.csv",sep=",",quote=F);

Error in stats.cal(object at d, object at d.bar, object at vec.false, object at p0,  :
  delta must be larger than 0.

If I put the delta number larger than 0, I cannot get all genes. The 
genes whose FDR is close to 1 is filtered out. But I need all info for 
all genes for further process.
I  found the stats.cal.R code, but don't know how to make it work,

Thanks in advance,

Wayne



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