[BioC] using mat.samp in siggenes

[James W. MacDonald]

Kathleen Kerr wrote:

> I am using the sam() function in siggenes and I 
> cannot find information about using the option mat.samp:
> 
>  mat.samp: a permutation matrix. If specified, this matrix will be used,
>         even if 'rand' and 'B' are specified.
> 
> I have a dataset with four treated samples and four control samples
> that are paired, so my class label is:
> cl=c(-1,-2,-3,-4, 1,2,3,4)
> 
> There are only 2^4=16 permutations, so I would just like to enumerate
> them.  The helpfile doesn't give any information about what the
> permutation matrix should look like.

The permutation matrix should be a 16 x 4 matrix of 1's and -1's

1 1 1 1
-1 1 1 1
1 -1 1 1
1 1 -1 1
etc

HTH,

Jim



> 
> I have tried the matrix with sixteen rows, each of which
> looks something like
> c(-1, 2, 3,-4, 1,-2,-3,4)
> but I get an error message that this is invalid.
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109