getGeneSets database versions #178

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1. ncborcherding commented on Jan 7, 2026

   

   ncborcherding

   on Jan 7, 2026

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   Hey Doug,

   The pulling of msigdb in the escape package is handled by the bioconductor package msigdb - https://bioconductor.org/packages/release/data/experiment/html/msigdb.html. Looking at the github repo (https://github.com/DavisLaboratory/msigdb) - it does not look like it has been updated for the recent versions. It might be worth it to bring this issue up there.

   In the meantime that does not really help your issue - there is a secondary package that is more actively maintained (msigdbr) - https://igordot.github.io/msigdbr/index.html (it looks like they have the updated version of msigdb you are looking for - https://igordot.github.io/msigdbr/news/index.html). If you go this route - the major step to make it compatible with escape is to form a list of the gene sets - I would use split() using the gs_name.

   Hope that helps,

   Nick
2. ncborcherding

   closed this as completedon Jan 7, 2026
3. dhcorn commented on Jan 12, 2026

   

   dhcorn

   on Jan 12, 2026

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   I am sorry to keep bothering you, but for some reason this still isnt working really well and I really think i am just missing something in the code.

   I am trying to run the msigdbr code then split it like you suggested. It looks like it is working just fine with the following code:

   gene_sets_Hall <- msigdbr(db_species = "MM", species = 'Mus musculus', 'MH')

   hallGene <- split(gene_sets_Hall, gene_sets_Hall$gs_name)
   head((hallGene))

   $HALLMARK_ADIPOGENESIS

   $HALLMARK_ALLOGRAFT_REJECTION

   $HALLMARK_ANDROGEN_RESPONSE

   $HALLMARK_ANGIOGENESIS

   $HALLMARK_APICAL_JUNCTION

   $HALLMARK_APICAL_SURFACE

   However when i run:

   eff.cells <- runEscape(Teff.cells,
   method = "GSVA",
   gene.sets = hallGene,
   groups = 500,
   min.size = 3,
   new.assay.name = "GSVA")

   I get the warning:

   Error in escape.matrix(input.data, gene.sets, method, groups, min.size, :
   No gene-sets meet the size threshold (min.size = 3)

   Though if i run:

   eff.cells <- runEscape(Teff.cells,
   method = "GSVA",
   gene.sets = hallGene$HALLMARK_GLYCOLYSIS,
   groups = 500,
   min.size = 3,
   new.assay.name = "GSVA")

   it will run. though i cant really look at anything because i dont really know what the output means.

   I guess my question is, do you see what i am doing wrong. i think it is me just not understanding the assay and not being particularly good at coding but any help would be much appreciated.

   Thanks

   Doug
4. ncborcherding commented on Jan 12, 2026

   

   ncborcherding

   on Jan 12, 2026

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   @dhcorn

   My mistake for not clarifying - escape is expecting a list of just gene symbols - right now you are feeding it a list of data.frame - here is a reproducible example to get the intended output:

   library(SeuratObject)
   library(msigdbr)
   library(dplyr)
   
   #Getting Human here to work with pbmc_small in SeuratObject
   gene_sets <- msigdbr()
   gene_sets_Hall <- gene_sets |> 
                       filter(gs_collection == "H")
   
   # Correct way to split
   hallGene <- split(gene_sets_Hall$gene_symbol, gene_sets_Hall$gs_name)
   head((hallGene))
     
   pbmc_small <- runEscape(pbmc_small,
                           method = "GSVA",
                           gene.sets = hallGene,
                           groups = 500,
                           min.size = 3,
                           new.assay.name = "GSVA")
   

   Hope that helps,
   Nick
5. dhcorn commented on Jan 12, 2026

   

   dhcorn

   on Jan 12, 2026

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   Oh ok, that makes sense. I thought it needed the whole dataframe from msigdbr.

   Thank you.