[R] the value of Delta

[jing]

Dear all,

I am running R 2.4.1.

> library(siggenes);
> library(multtest);
> cl<-rep(c(0,1),c(3,3));
> sub<-exprs(AffyExpData[,c(1:3,7:9)]);
> gn<-geneNames(AffyRAwData);
> sam.out<-sam(sub,cl,rand=123,gene.names=gn);

We're doing 20 complete permutations

> sam.out
SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances 
 
   Delta    p0  False Called   FDR
1    0.1 0.929 292.25    293 0.927
2    0.4 0.929  43.60     56 0.724
3    0.7 0.929  12.25     20 0.569
4    1.0 0.929   7.25     14 0.481
5    1.3 0.929   2.60      7 0.345
6    1.7 0.929   1.30      5 0.242
7    2.0 0.929   1.30      5 0.242
8    2.3 0.929   0.45      2 0.209
9    2.6 0.929   0.45      2 0.209
10   2.9 0.929   0.45      2 0.209

> sum.sam.out<-summary(sam.out,1,ll=FALSE);
> sum.sam.out$row.sig.genes;
NULL
> sum.sam.out<-summary(sam.out,0.1,ll=FALSE);
> sum.sam.out$row.sig.genes;
NULL
> sum.sam.out<-summary(sam.out,0.00000000001,ll=FALSE);
> sum.sam.out$row.sig.genes;
NULL
> sum.sam.out<-summary(sam.out,1000,ll=FALSE);
> sum.sam.out$row.sig.genes;
NULL
   

Any value of Delta I chosen: 1000,1,0,1 0.00000000001, the outcome is NULL.

Any help or suggestions that you can provide will be greatly appreciated.

Qing