[BioC] siggenes permutation count problem

paul.boutros@utoronto.ca paul.boutros at utoronto.ca
Sat Jan 7 01:26:46 CET 2006


I'm having some troubles interpreting how/why siggenes performed a certain 
number of permutations on my dataset.  This is an affy dataset that was 
normalized by:

data <- ReadAffy(filenames=cel.files, phenoData="phenodata.txt");
eset <- expresso(data, normalize.method="constant", bgcorrect.method="none", 
pmcorrect.method="mas", summary.method="avgdiff");

I realize that the normalization is a bit unusual: this study is actually 
testing a range of normalization methods.  This is a two-class experiment with 
3 arrays in each group:

> eset;
Expression Set (exprSet) with 
        22690 genes
        6 samples
                 phenoData object with 1 variables and 6 cases
                Group: read from file
> design;
[1] 1 1 0 1 0 0

So to do a SAM-like analysis I used:
SAM.data <- sam(data=eset, cl=design, var.equal=FALSE, B=1000);

And I expected there to be 6! = 720 total possible permutations.  So I was 
surprised to get this output:
> SAM.data <- sam(data=eset, cl=design, var.equal=FALSE, B=1000);

We're doing 20 complete permutations

Why does siggenes think there are only 20 complete permutations to be used?  
Have I done something wrong, or is my understanding of how the permutations are 
done in error?

This is R 2.2.1 and siggenes 1.4.0 on WinXP.


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