[BioC] Question on the paired ttest in multtest package

James W. MacDonald jmacdon at med.umich.edu
Thu Jul 30 19:32:09 CEST 2009

Hi Anqi,

Anqi wrote:
> Dear Bioconductor developers,
> I am using multtest package to do some analysis. 
> I am using the function mt.maxT/mt.minP to do some paired t-test. 
> I email to ask how does the function recognize "paires" out of a classlabel like c(0,1,0,1,0,1,0,1,0,1,....,0,1). 
> Does the package pair the first "0" with the first "1"? 

Yes. You can sort of deduce this from the help page. So if you look at 
the help for mt.maxT you can see that the help for the classlabel 
argument states that

'The observations are ordered by block, and within each block,
  they are labeled using the integers 0 to k-1. '

In addition, there is an example

# Permutation adjusted p-values for maxT procedure with paired t-statistics



> Much thanks and best regards,
> Anqi
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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