Re: [R] the value of Delta

From: Christoph Buser <buser_at_stat.math.ethz.ch>
Date: Tue 23 Jan 2007 - 09:17:05 GMT

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@row.sig.genes

instead of "$"

Hope this helps

Christoph


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Christoph Buser <buser@stat.math.ethz.ch> Seminar fuer Statistik, LEO C13
ETH Zurich	8092 Zurich	 SWITZERLAND
phone: x-41-44-632-4673		fax: 632-1228

http://stat.ethz.ch/~buser/

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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> and provide commented, minimal, self-contained, reproducible code.



R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Tue Jan 23 20:21:47 2007

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