[BioC] multtest

[Stefanie Scheid]

Hi,

after using multtest to calculate Wilcoxon test statistics for original
and for permuted class labels, three questions appeared:

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").

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")?

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?


Thanks a lot,
Stefanie.



index <- c(rep(0,5),rep(1,5))
value <- c(3,6.5,2,1,1.5,6,9,8,0,3.5)
expr <- t(matrix(value,10,2))  # a very correlated expression matrix :-)

stat.orig <- mt.teststat(expr,index,test="wilcoxon")

stat.perm1 <- apply(expr, 1, mt.sample.teststat, index, test="wilcoxon",
B=10, nonpara="n", fixed.seed.sampling="n")

stat.perm2 <- apply(expr, 1, mt.sample.teststat, index, test="wilcoxon",
B=10, nonpara="n", fixed.seed.sampling="y")


a1 <- sum(rank(expr[1,])[6:10])
a2 <- (sum(rank(expr[1,])[6:10])-5*11/2)/sqrt(25*11/12)

b1 <- wilcox.test(value[1:5],value[6:10])$statistic
b2 <- sum(rank(expr[1,])[1:5])-5*6/2




---

Stefanie Scheid

Max Planck Institute for Molecular Genetics
Dept. of Computational Molecular Biology
Ihnestraße 63-73
D-14195 Berlin, Germany

phone: +49 (0)30 8413 1178
fax:   +49 (0)30 8413 1152

http://www.molgen.mpg.de/~scheid
email: stefanie.scheid at molgen.mpg.de