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