[R] the value of Delta

[Christoph Buser]

I have not installed the package "siggenes", but from the manual
on" 

http://www.ugrad.stat.ubc.ca/R/library/siggenes/

I assume it is programmed as an S4 class since they use 

sum.sam.out at row.sig.genes

instead of "$"

Hope this helps

Christoph

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Christoph Buser <buser at stat.math.ethz.ch>
Seminar fuer Statistik, LEO C13
ETH Zurich	8092 Zurich	 SWITZERLAND
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jing writes:
 > 
 > 
 > 
 > 
 > 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
 > 
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