Update in the gage RNA-seq pathway analysis joint workflow

bigmw · 02-12-2014, 04:27 PM

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/rel...html/gage.html
http://bioconductor.org/packages/rel...eqWorkflow.pdf

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
RNA-Seq Pathway and Gene-set Analysis Workflows in R/Bioconductor with GAGE/Pathview	bigmw	Bioinformatics	92	11-17-2015 10:48 AM
Splicing Analysis in Partek RNA-Seq workflow	xguo	Bioinformatics	1	12-21-2009 10:06 AM

02-12-2014, 04:27 PM	#1
bigmw Senior Member Location: US Join Date: Aug 2013 Posts: 123	Update in the gage RNA-seq pathway analysis joint workflow 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/rel...html/gage.html http://bioconductor.org/packages/rel...eqWorkflow.pdf