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 <satijalab/seurat#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?

[mjquackenbush]

Following up here, still getting same issue.

[ncborcherding]

@mjquackenbush

This should be installed with the most recent version of escape in the github repo and in the bioconductor release. Please let me know if upgrading doesn't fix the issue and follow up with a repro example would be immensely helpful/

Nick

[mjquackenbush]

@ncborcherding I installed the newest version of escape listed on the github repository using bioconductor and I am still getting the same error detailed above.

escape.gene.sets <- getGeneSets(library = "H", species = 'Mus musculus')

scRep_example <- runEscape(scRep_example,

•                        method = "ssGSEA",
  

•                        gene.sets = escape.gene.sets, 
  

•                        groups = 1000, 
  

•                        min.size = 3,
  

•                        new.assay.name = "escape.ssGSEA")
  

[1] "Using sets of 1000 cells. Running 16 times."
Warning: Layer counts isn't present in the assay object; returning NULL

My seurat object is Version 5.3.0.

Version(scRep_example)
[1] ‘5.3.0’

I am including a screenshot of inspecting the seurat object where the escape.ssGSEA assay is stored.

[ncborcherding]

@mjquackenbush,

Sorry to clarify - escape is running and storing the outputs, but Seurat is giving you a warning. So you are fine to go forward, because there is a difference between Seurat v5 and v3 assays still that exist in 5.3.0 of Seurat, this is more of a annoyance than anything.

Apologies for the confusion

Nick