Error message: selected chip does not match MSigDB version

[A MM]

Hello again,

I would appreciate it if you could help me with the following error message:

"The selected CHIP does not match the version of the MSigDB collection selected. Some gene identifiers may not be mapped".

I have selected:

Gene set: mh.all.v2025.1.Mm.symbols.gmt

Chip platform: Clariom_S_Mouse.r1_MSigDB.v7.1_REMAPPED_PATCH.chip

I have seen that MSigDB v7.1 is from 2020, but the drop-down menu for Gene Sets within the GSEA software only goes back until 2022.

Which gene set version should I use?

Thank you again,

AMalia

[Anthony Castanza]

Hi Amalia,

Unfortunately our ability to support mappings for the Clariom arrays is restricted by the array manufacturers current licensing terms and we don't have access to the native-space annotations to provide a file for use with the mouse database directly.

In order to run your Clariom data against the current version of MSigDB, you would need to use the human collections, with the ortholog mapping chip available here:

https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Mouse_Clariom_S.r1_Human_Orthologs_MSigDB.v2025.1.Hs_REMAPPED_PATCH.chip

You can download this file, and load it in to GSEA the same way you load in your data files, then it should appear in the local chips tab of the file selector.
You'll still see the warning about the version match, but it can be safely ignored with the h.all .v2025.1.Hs.symbols.gmt file, or any other human collection files.

Let me know if you have any additional questions, and we apologize for the complication here.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego