Question: Typo / Mistyped in rWikipathways - 4. Pathway Analysis? (GSEA) / NES <-1 instead of NES < 1 for downregulated genes
2
10 months ago by
Fischer-philipp20 wrote:

Hey everyone,

I was reading the documentation of rWikipathways( check link below) when I think I encountered a typo.

https://bioconductor.org/packages/release/bioc/vignettes/rWikiPathways/inst/doc/Pathway-Analysis.html

After running GSEA() one is to distinguish which pathways are enriched for upregulated and which for downregulated genes.

The following code is a copy of the assumed typo.

## 4.WikiPathways

gwp.sig.lung.expr.df[which(gwp.sig.lung.expr.df$NES>1),] #pathways enriched for upregulated lung cancer genes (1) gwp.sig.lung.expr.df[which(gwp.sig.lung.expr.df$NES<1),] #pathways enriched for downregulated lung cancer genes (2)

In code line (2): Shouldn't it be ...$NES < -1 instead of$NES < 1?

modified 6 months ago by alex.pico0 • written 10 months ago by Fischer-philipp20
Answer: Typo / Mistyped in rWikipathways - 4. Pathway Analysis? (GSEA) / NES <-1 instead
0
6 months ago by
alex.pico0 wrote:

Yes. This has been fixed and will be in the next release at the end of the month. Thanks for catching this!