Dear all,

I have some questions relating to PGSEA package and GSEA method and hope to
get some replies:


1. After reading the following paper, I think the theoretical basis for
PGSEA is very different from GSEA (Broad, MIT).  So, my first question is,
is there a package in bioconductor running GSEA? (I used some R version
downloaded from GSEA website before, though).

http://www.biomedcentral.com/1471-2105/6/144

2. The paper above mentioned comparison of two "groups" of samples for a
specific pre-defined gene set, but not individual samples. For the case of
cancer data, for example, I assume PGSEA uses normal patients' medians or
something as reference to calculate fold change (ratio data) for each cancer
patient, then run PGSEA. Is this way PGSEA calculates "enriched" gene sets
for each sample? I think the question boils down to, how to calculate the
fold change or ratio data for PGSEA, esp. in case of experiments with 2
factor design and intensity data? (is it a challenging question?)

3. From PGSEA command as below,

x <- PGSEA(...);

is x a matrix of z-scores described in the paper?

thanks,

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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