Dear list,
I'm new using GSEAbase and I've seen some examples given in 
"Bioconductor case studies" book. A data example is given according to 
the following steps:

    * Nonspecific filtering on expression data object.
    * Building the GeneSetCollection using KEGG (for example).
    * Compute the per gene test statistics using t-test
    * Use of a permutation test to assess which genes have an unusually
      large absolute value of the distribution.

My question is: can we use any kind of statistic? For example, moderated 
t-statistic using limma?I know that limma uses the eBayes function, 
which employs information from all genes to arrive at more stable 
estimates of each individual gene's variance and I don't know if, in 
GSEA context, it is correct to use this moderated statistic which takes 
into account all the genes (it is not like the "standard" per gene 
statistic t-test).

Thanks,
Javier



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