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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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GSEA background sets of genes #159

Closed sofiapuvogel closed 3 years ago

sofiapuvogel commented 3 years ago

Dear MAST team, I am performing GESEA with MAST, but it is not clear to me what the program uses as "background gene sets". I am following the MAIT Analysis tutorial, with min_gene_in_module <- 5. Best regards, Sofía

amcdavid commented 3 years ago

Hi Sofia,

These are competitive tests, so the background is everything that is in the SingleCellAssay object, that is not in the set currently being tested. The 2015 paper has the details: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0844-5#Sec12

On Jun 2, 2021, at 11:09 AM, sofiapuvogel @.***> wrote:

Dear MAST team, I am performing GESEA with MAST, but it is not clear to me what the program uses as "background gene sets". I am following the MAIT Analysis tutorial, with min_gene_in_module <- 5. Best regards, Sofía

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sofiapuvogel commented 3 years ago

Thanks!