Which Chip platform is the right one?

[Leonard Kaps]

Hi,

I encounter error 1005 when I run GESA.

I guess I have the wrong chip platform.

Which platform is the right one to run my dataset (attached)?

Thank you very much 

Best

Leo

[Anthony Castanza]

Hi Leonard,

This dataset would be using the Mouse_Ensembl_Gene_ID chip file, however there is one small issue.
The dataset as it is currently has versioned Ensembl IDs; ENSMUSG00000000103.12
The version is the suffix (".12" for this gene), and you will need to strip all the suffixes in order for the genes to be recognized by the Ensembl chips that we provide.

Sorry about the additional complication! Let me know if you have any difficulty doing this. In excel it should be  reasonably straightforward with the text to columns tool.

-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 very much!

I had success running the broad gene set

mh.all.v2023.2.Mm.symbols.gmt

Unfortunately there is still an issue with the gene set I am interested in: HALLMARK_ANGIOGENESIS.v2023.2.Mm.gm

Error : the selected CHIP does not match the version of the MSigDB collection selected. Some identifiers may not be mapped.

I guess I need another Chip platform for this gene set

Best

Leo

[Anthony Castanza]

Hi Leonard,

If you successfully ran the mh.all file then that should have already included the Angiogenesis set, you shouldn't need to run it separately and it should definitely work with the same chip as that .mh.all file.

I suspect that the message you received is a result of a known bug that can occur in the version matching check that we recently added when some files are reloaded from the application cache.

Was this actually returned as an error message or just as a warning that you could click through? If it was just a warning it can be safely ignored. If it was an actual blocking error message downloading and loading in both the chip and gene set files from local copies should allow you to bypass it.

-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]

Perfect thank you very much for your help!