GSEA.mean.t {SAGx}R Documentation

Gene Set Enrichment Analysis using output from samroc

Description

Based on a list of gene sets, e.g. pathways, in terms Affymtrix identifiers, these sets are ranked with respect to regulation as measured by an effect in a linear model using the SAM statistic.

Usage

GSEA.mean.t(data = X, samroc = samroc.res, probeset = probeset, 
pway = kegg, absolute = TRUE, two.side = FALSE, cutoff = c(5,Inf), B = 1000, smooth = FALSE)

Arguments

data data matrix
samroc an object of class samroc.result
probeset the Affymetrix identifiers
pway a list of pathways or gene sets
absolute if TRUE the absolute value of the absolute value of the samroc test statistic is used. Currently this is the only option
two.side if TRUE a two-sided test is performed. Currently only one-sided test allowd
cutoff Gene sets with the number of members not falling within the interval given by cutoff are excluded
B the number of permutations
smooth if TRUE smoothing of SEs is performed. Currently this is not permitted

Value

A vector of p-values

Note

Experimental function

Author(s)

Per Broberg

References

Tian, Lu and Greenberg, Steven A. and Kong, Sek Won and Altschuler, Josiah and Kohane, Isaac S. and Park, Peter J. (2005) Discovering statistically significant pathways in expression profiling studies, PNAS Vol. 102, nr. 38, pp. 13544-13549


[Package SAGx version 1.7.1 Index]