[BioC] multtest

[Sandrine Dudoit]

Hi Stefanie,

Thank you for the feedback. We have updated the code and fixed
the help pages to clarify the issues you raised about the computation
of the Wilcoxon test statistic. The revised package is available
under "Developmental Packages".

Below are answers to your three questions.

> 1. What is calculated by mt.teststat ("stat.orig")?
> The Wilcoxon statistic is defined as the ranksum of one of the two samples
> after joining. In my simple example "a1" is the ranksum which is not equal
> to "stat.orig". Actually, the function wilcox.test gives a third result
> which is the ranksum minus its theoretical minimum ("b1"=="b2").

The function now computes the centered and scaled version of the
Wilcoxon statistic.

[sum ranks for sample 1 - n1*(n1+n2+1)/2]/sqrt(n1*n2*(n1+n2+1)/12)

We have also corrected the cut-and-paste error in the help file.

> 2. What is calculated my mt.sample.teststat ("stat.perm")?
> Here, the calculated Wilcoxon statistics seem to be standardized. Why is
> the original value not standardized ("stat.orig"!="a2")?

This function also computes the centered and scaled version of the
Wilcoxon statistic as in  mt.teststat.

> 3. What is the difference between fixed.seed.sampling="y" and "n"?
> Each time I run the example the permuted values stay fixed. Is there way
> to calculate values with random seeds?

This option is only meaningful for the minP procedure.
Details are given in Remarks 2.(a) and 2.(b) in Section 4.4.3  of the tech
report http://www.stat.berkeley.edu/~gyc/633.pdf.
In summary, there are two different ways to force each row of the T,
P, and Q matrices to contain the same order for the B permutations.
If we use fixed.seed.sampling="y", then each time we go from one
row to another row, we use the same random seed.
If we use fixed.seed.sampling="n", we store the B permutation
configurations into memory and for each row read these from memory.

Best regards,
Sandrine

-------------------------------------------------------------------------------
Sandrine Dudoit, Ph.D.               E-mail: sandrine at stat.berkeley.edu
Assistant Professor                  Tel: (510) 643-1108
Division of Biostatistics            Fax: (510) 643-5163
School of Public Health		     http://www.stat.berkeley.edu/~sandrine
University of California, Berkeley
140 Earl Warren Hall, #7360
Berkeley, CA 94720-7360