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ncborcherding / escape

Easy single cell analysis platform for enrichment
https://www.borch.dev/uploads/screpertoire/articles/running_escape
MIT License
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Error when looking for Differential Enrichment using FindAllMarkers #126

Closed SunnyHelperT closed 1 month ago

SunnyHelperT commented 1 month ago

Hi Dr. Borcherding,

Thank you for creating this extremely helpful package for single cell GSEA. I'm somewhat new to R and ran into this error by following this vignette -- https://www.bioconductor.org/packages/release/bioc/vignettes/escape/inst/doc/vignette.html#6_Conclusions

I would appreciate it if you can help me troubleshoot this. Thank you so much!

all.markers <- FindAllMarkers(sce_PMN_MDSC_GS_H_pos,

  • assay = "escape.ssGSEA_normalized",
  • min.pct = 0,
  • logfc.threshold = 0)

Error in UseMethod(generic = "Idents", object = object) : no applicable method for 'Idents' applied to an object of class "c('SingleCellExperiment', 'RangedSummarizedExperiment', 'GsvaExprData', 'SummarizedExperiment', 'RectangularData', 'Vector', 'Annotated', 'vector_OR_Vector')"

Update: Closed issue - single cell experiment object was used instead of seurat. Sorry for the trouble!