error from msigdbr

Question

[hamid.gaikani]

Hi

I am trying to use msigdbr in my ran-seq script in order to do GSEA. My model is yeast so I am trying this code:

yeast_gsea <- msigdbr(species = "Saccharomyces cerevisiae") #gets all collections/signatures with yeast
yeast_gsea %>%   dplyr::distinct(gs_cat, gs_subcat) %>%   dplyr::arrange(gs_cat, gs_subcat)
#choose a specific msigdb collection/subcollection yeast_gsea_c5 <- msigdbr(species = "Saccharomyces cerevisiae", category = "C5") %>%     dplyr::select(gs_name, gene_symbol)

Everything works without error but the enrichments I get at the end has terms for human (like leukemia and Sprengel), so I am sure something is going wrong but I am clueless. I am a beginner and I would appreciate any help.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

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Answer 1

[Papyrus]

This package uses the MSigDB gene sets which have a focus on human (and more recently, mouse). So for other species, as far as I know the pathways have been "translated" from these gene sets to homologous genes using HUGO. It can be the case that some of these pathways do not make sense in your species. See the vignette.

[hamid.gaikani]

Thanks, Papyrus it makes sense. Can I ask what would you do? should I not use msigdb and use more traditional GSEA? I would appreciate any feedback if you have expertise.

[Papyrus]

I think you're confusing concepts here. MSigDB are the gene sets that you use and GSEA is the analysis method. There is no problem with the analysis method, but if you don't like the gene sets you can try to look for other databases of gene sets maybe more related to your species.

[hamid.gaikani]

thanks, Papyrus. It's crystal clear now. I downlaoded a yeast gene set on gProfiler and it works much better. I appreciate your help (: