Clariom D mouse analysis

[Aushia Tanzih Alhaq]

Hi all,

I'm having a problem to analyze mouse Clariom D array with GSEA. It keeps saying 'The collapsed dataset  was empty when used with chip." Is mouse Clariom D not supported by GSEA chip platform?

Thanks,

Aushia

NHRI, Taiwan

[Anthony Castanza]

Hi Aushia,

Are you using the Clariom chips from here: https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations_legacy/

(for the version of MSigDB that you're using), and additionally did you set the Collapse/Remap parameter to "Collapse"? If you don't change this parameter in addition to providing a chip file then the chip file isn't actually used.

If you've checked you're using the correct version of chip from the annotations_legacy repository, and you're setting the "Collapse" parameter, then it's possible there is some issue with your input data, such as not representing the complete clariom array panel, or using some identifier other than the transcript cluster ID (which is, if I recall correctly, what these chips use).

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

[Aushia Tanzih Alhaq]

Hi Anthony,

Thanks a lot for your prompt answer. I used the 'Collapse' parameter, but chose Mouse ENSEMBL Gene ID and Mouse Gene Symbol Remapping Human Orthologs (in the default options of GSEA). 

The analysis is working fine as I upload the Clariom D chip platform from the annotation repository you have provided. 

Much appreciated,

Aushia