[BioC] a couple of questions on PGSEA package and GSEA

[Furge, Kyle]

1. Yes, the GSEA and PGSEA methods use different calculations to assess gene
set enrichment.  I am not aware of another implementation of GSEA other than
the one available from the GSEA website, but I have not looked in a while.

2. It is really your preference on how to calculate ratios. I typically
sweep the median intensity value of the reference set through each test
sample individually. I do this because I am often interested in looking at
individual sample variances. You could also average the test samples and
average the reference samples and then construct a single ratio. It is
really your preference.

3. The default settings of PGSEA returns a matrix of z-scores as described
-- assuming that the test samples were not first not combined in a single
sample by averaging as discussed in 2. However, the results matrix could
contain NAs as the PGSEA function has an option to filter the results based
on a p.value cutoff.  Scores that fall below the p.value threshold will be
set to NA in the matrix.  If you don't like this behavior, make sure to turn
of that option in the PGSEA function call.

-kyle



On 9/4/08 9:53 PM, "Weiwei Shi" <helprhelp at gmail.com> wrote:

> 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,


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