[BioC] stat/math question on Category vignette

[Mark W Kimpel]

I am working my way through the Category vignette and have a question as 
to how the t statistics for categories are computed from the incidence 
matrix and individual probeset t-statistics. The code that does this can 
be found on the bottom of page 3 (development version vignette) and is 
as follows:

There are 135 pathways (categories)...
A = AmER2 %*% tobs$statistic
A = tA/sqrt(rs2)
ames(tA) = row.names(AmER2)

I know this is matrix multiplication, but don't know the mathematical or 
statistical basis for the computation. I am interested in turning the t 
statistic values in tA into p values, so I need to know the df. for each 
resultant t. Is that the rs2?

This is know doubt a simple question for the statisticians in the group, 
but not for me! :) Thanks for your help,

Mark

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Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

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