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

[Luo Weijun]

Juliet,
You may try the gage package. Check the help info on main function:
?gage
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)

HTH,
Weijun


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

All,

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?

Thanks,

Juliet