The molecular signatures database (MSigDB) in R

Question

[Kelly]

I'm trying to use the msigdb package, but I can't seem to access the EH9632 resource. When I call msigdb::getMsigdb(), it only fetches up to EH8300. From what I understand in the official vignette, the most recent version of MSigDB should be v 1.9.x, but my setup seems to be defaulting to older versions (e.g., 1.14.0 instead of 1.19.x). I've tried updating the package and Bioconductor version, but I haven't been able to force access to the EH9632 resource. Code I'm using:

if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")

BiocManager::install("msigdb", force = TRUE)

packageVersion("msigdb")

library(msigdb)   
library(ExperimentHub) 
library(GSEABase)     

eh <- ExperimentHub()

msigdb_records <- query(eh, "msigdb")

print(msigdb_records)

Any help on how to access the correct version or force download of EH9632 would be greatly appreciated!

Answer 1

[marco.barr]

Hi, with the current version of Bioconductor and msigdb I was able to access the EH9632 dataset you requested. I'm sharing with you the versions I have and the commands I used. Try with these versions as well. I’m also attaching the dataset in case you’re unable to access it if necessary.

library(msigdb)   
library(ExperimentHub) 
library(GSEABase)

version
platform       x86_64-w64-mingw32               
arch           x86_64                           
os             mingw32                          
crt            ucrt                             
system         x86_64, mingw32                  
status                                          
major          4                                
minor          5.0                              
year           2025                             
month          04                               
day            11                               
svn rev        88135                            
language       R                                
version.string R version 4.5.0 (2025-04-11 ucrt)
nickname       How About a Twenty-Six

package.version("BiocManager")
[1] "1.30.25"

package.version("msigdb")
[1] "1.16.0"

eh <- ExperimentHub()
msigdb_records <- query(eh, "msigdb")
print(msigdb_records)

ExperimentHub with 51 records
# snapshotDate(): 2025-04-12
# $dataprovider: Broad Institute, Emory University, EBI, NA
# $species: Homo sapiens, Mus musculus
# $rdataclass: GSEABase::GeneSetCollection, data.frame, list
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH5421"]]' 

           title                   
  EH5421 | msigdb.v7.2.hs.SYM      
  EH5422 | msigdb.v7.2.hs.EZID     
  EH5423 | msigdb.v7.2.mm.SYM      
  EH5424 | msigdb.v7.2.mm.EZID     
  EH6727 | MSigDB C8 MANNO MIDBRAIN
  ...      ...                     
  EH8298 | msigdb.v7.5.1.mm.idf    
  EH8299 | msigdb.v7.5.1.mm.SYM    
  EH8300 | imex_hsmm_0722          
  EH9632 | MSigDB v2024.1.Hs       
  EH9633 | MSigDB v2024.1.Mm

EH9632 <- eh[["EH9632"]]
msigdbeh not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
Install msigdbeh [yes/no] no
loading from cache

I hope this helps,

Best regards

Marco