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bhklab / genefu

R package providing various functions relevant for gene expression analysis with emphasis on breast cancer.
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Subtyping mouse samples #21

Closed maringa780 closed 2 years ago

maringa780 commented 3 years ago

Hello,

I'm trying to subtype (PAM50) mouse breast cancer samples (RNAseq) and I was wondering if Genefu accounts for the fact that the genes in mouse have different gene id compared to their human orthologs. Please advice. Thanks.

ChristopherEeles commented 2 years ago

Hi @maringa780,

As far as I know our gene signatures would all use human based gene ids. If I remember correctly, we use gene symbols.

The simplest solution would be to map the mouse gene symbols to human gene symbols before using the classifier.

Best, Christopher Eeles Software Developer Benjamin Haibe-Kains Lab PM-Research | University Health Network

ChristopherEeles commented 2 years ago

Hi @maringa780,

Just read through some of the documentation. The type of gene identifier depends on the classifier used. Some use gene symbol and some use Entrez gene id.

For more information please see ?molecular.subtyping in the R console. That will bring up documentation explaining the requirements for using the function.

Best, Chirs