Dear gage users: There were some typos in page 11 of the ?RNA-seq Data Pathway and Gene-set Analysis Workflows? vignette (gage 2.12.1, December 20, 2013). This only occurred with the joint workflow details (with DESeq/DESeq2, edgeR, Limma or Cufflinks). RNA-Seq pathway analyses following the native workflow or the Quick Start are not affected. Original code was: .. sel.l <- cnts.kegg.p$less[, "q.val"] < 0.1 & !is.na(cnts.kegg.p$less[,"q.val"]) path.ids.l <- rownames(cnts.kegg.p$less)[sel.l] .. The typos resulted in ?Error: object 'cnts.kegg.p' not found?. Here cnts.kegg.p should be fc.kegg.p instead. The typos have been corrected in the updated package (gage 2.12.2): http://bioconductor.org/packages/release/bioc/html/gage.html Sorry for the confusion. Weijun