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Luo Weijun ★ 1.6k
@luo-weijun-1783
Last seen 9 months ago
United States
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 > > > ???
gage gage • 887 views
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