[BioC] enrichment packages that accept t-stat (or related stat) as input

Luo Weijun luo_weijun at yahoo.com
Wed Aug 28 21:07:46 CEST 2013

You may try the gage package. Check the help info on main function:
Gage function accepts as input data the 1-column matrix or vector of your test statistics from your upstream gene level analysis. GAGE test for pathway level changes using t test, so t-statistics would fits well.
Following the vignette example, you may do something like:
gse16873.1sample.kegg.p <- gage(gse16873[,1], gsets = kegg.gs, ref = NULL, samp = NULL)


On Wed, 8/28/13, Juliet Hannah wrote:


I am looking for an Bioconductor enrichment package that does something
similar to GSEA for pre-computed test statistics. This method would not
rely on a cutoff. That is, rather than passing an expression matrix, one
can compute summarizes outside of the package (such as a limma t), and then
pass these. Any suggestions?



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