Issue with runEscape() and counts Layer

[monikaramos]

Hi there,

I'm encountering the following error when running runEscape() but not when I run escape.matrix()

pbmc_small <- runEscape(pbmc_small,

• method = "ssGSEA",
• gene.sets = gene.sets,
• groups = 1000,
• min.size = 5,
• new.assay.name = "escape.ssGSEA") [1] "Using sets of 1000 cells. Running 1 times." Warning: Layer counts isn't present in the assay object; returning NULL

I am working with a seurat v5 object and it will successfully run when I use the escape.matrix function. Unfortunately, I would like to be able to use the runEscape function so I can have more ease with and more plotting functions. Please advise, thank you!

I've updated the escape package too.

Version R 4.4

[ncborcherding]

Hey @monikaramos,

This appears to be an issue with the Seurat version - find out more info here.

In the meantime, you can add the output of escape.matrix() to your Seurat object using:

new.assay <- CreateAssayObject(data = as.matrix(t(enrichment.results))))

SeuratObj[["escape"]] <- new.assay)

Hope that helps, let me know if you have any other questions.

Thanks, Nick

[monikaramos]

Thank you for your response! Unfortunately, in doing so I still get the following warning, is this okay?

new.assay <- CreateAssayObject(data = as.matrix(t(enrichment.scores))) pbmc_small[["escape"]] <- new.assay Warning: Layer counts isn't present in the assay object; returning NULL

Also, is the enrichment score calculation done on the seurat v5's count assay (raw) or the data assay (normalized)?

thanks for your help.

On Mon, Aug 19, 2024 at 3:40 AM theHumanBorch @.***> wrote:

Hey @monikaramos https://github.com/monikaramos,

This appears to be an issue with the Seurat version - find out more info here https://github.com/satijalab/seurat/issues/8938.

In the meantime, you can add the output of escape.matrix() to your Seurat object using:

new.assay <- CreateAssayObject(data = as.matrix(t(enrichment.results))))

SeuratObj[["escape"]] <- new.assay)

Hope that helps, let me know if you have any other questions.

Thanks, Nick

— Reply to this email directly, view it on GitHub https://github.com/ncborcherding/escape/issues/114#issuecomment-2296260994, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUKNITMKAYV3FLPUU6THO73ZSHDRPAVCNFSM6AAAAABMW3EBSKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJWGI3DAOJZGQ . You are receiving this because you were mentioned.Message ID: @.***>

[yeroslaviz]

I'm getting the same error here. Was this solved?