Selected CHIP is not compatible with the selected gene set species

[Leonard Kaps]

Hi,

I encounter the following problem when I run GESA with this database (pls see txt and cls file):

 

"Selected CHIP is not compatible with the selected gene set species" (pls see pdf attachment).

 

Could you give me an idea how to solve the problem, pls?

I have already tried several permutations but still the problem occurs.

I guess the selected chip platform migh be the problem.

 

THX

 

Best

L Kaps

[Castanza, Anthony]

Hello,

So, the error here is that you’ve selected the mh.all.v2023.1.Mm.symbols.gmt file (Mouse Hallmarks from MSigDB v2023.1 provided in Mouse Gene Symbols), however, the CHIP file you’re specifying is Mouse_Gene_Symbol_Remapping_MSigDB.v7.0.chip (Mouse Gene Symbol Remapping from Mouse to Human Gene Symbols for MSigDB v7.0). As the error message indicates, these are not compatible files. They are not the same mapped namespace of gene symbols, and they are not the same MSigDB version.

In order to run this analysis, you need to select the “Mouse_Gene_Symbol_Remapping_MSigDB.v2023.1.Mm.chip” file from the second (Mouse Collection Chips (MSigDB)) tab of the Chip file selection dialogue. This us both the same mapped target species and the same MSigDB version.

 

Let me know if you continue to encounter issues after making this adjustment.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Leonard Kaps]

Thank you! I could solve the problem when I canged the gene names into capital letters. But I think the mapping is still an issue. Can you check my next issue - pls see my question in the thread of Neda Mahboobnia ?

Best

Leo

[Anthony Castanza]

You should not just uppercases the gene names. You should use the appropriate mapping chip file as I indicated in my previous reply. Uppercasing the gene symbols will result in mapping errors and erroneous dropouts.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/a49d09c5-7136-4ac1-b04a-5594a9c3ddc6n%40googlegroups.com.