[BioC] Update in the gage RNA-seq pathway analysis joint workflow

[Luo Weijun]

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