[BioC] gage

[Luo Weijun]

Hi Pietro,
In gage package, function essGene extract essential member genes in a gene set, which are the genes contribute to the overall significance of a gene set. Function essGene is used together with geneData generate heatmap, scatterplot and data table for gene sets. To get the details, type:
?essGene

The package PDF vignette also shows a series of examples. To see a full list of relevant functions and introduction, type in:
library(help=gage)
HTH,
Weijun


--- On Tue, 4/24/12, Pietro Zoppoli <pz2173 at columbia.edu> wrote:

> From: Pietro Zoppoli <pz2173 at columbia.edu>
> Subject: gage
> To: "luo_weijun at yahoo.com" <luo_weijun at yahoo.com>
> Date: Tuesday, April 24, 2012, 10:47 AM
> Dear Dr. Luo,
> I'm using your package gage on R and it works very well.
> I use it with "saaTest = gs.KSTest" ,so I'm doing GSEA on a
> pre-ranked list.
> In the output I find (among the others) the "q-value" and
> the "set.size".
> 
> Is there a way to obtain the leading edge point (the point
> where the running sum reaches its maximum deviation from
> zero ) using gage ?
> 
> In  (Subramanian et al) "A Gene set enrichment
> analysis: a knowledge-based approach for interpreting
> genome-wide expression profiles. Proc Natl Acad Sci U S
> A.(2005)
> They define it as:
> "We define the leading-edge subset to be those genes in the
> gene set S that appear in the ranked list L at, or before,
> the point where the running sum reaches its maximum
> deviation from zero. The leading-edge subset can be
> interpreted as the core of a gene set that accounts for the
> enrichment signal. "
> 
> Thanks in advance,
> Pietro Zoppoli
> 
> 
>