Typo / Mistyped in rWikipathways - 4. Pathway Analysis? (GSEA) / NES <-1 instead of NES < 1 for downregulated genes
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@fischer-philipp-18490
Last seen 2.5 years ago
Austria

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?

Thanks for your answers.

typo NES rwikipathways downregulated genes gene set enrichment analysis • 1.0k views
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alex.pico ▴ 30
@alexpico-15339
Last seen 10 weeks ago
United States

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

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