James MacDonald jmacdon at med.umich.edu
Mon Dec 8 15:05:52 MET 2003

If you are simply looking to calculate some permutation adjusted
p-values, you should look at the help for either multtest or siggenes.
Both packages have very clear help pages.

I am not sure how (or why) you want to bootstrap your data, but if you
really want to do this, you are going to have to figure it out on your
own because there are no 'canned' functions to do what you want.

I would recommend using either multtest or siggenes.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Kevin Dawson" <kdawson at ucdavis.edu> 12/07/03 07:02PM >>>

Does any one know how to calculate the BOOTSTRAP-adjusted p-values.

The normalized expression values are in the 22283-by-16 matrix expr.

The 16-long dclass vector contains the classifiers [0 1 0 1 0 1 0 ...]

The goal is to compute the 22283-long vector with the adjusted
Does any one have expericence with boot() or another procedure?

Thank you for your help.

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