AvgExpression error in seurat: invalid name for slot of class “Assay5”: check.matrix

Question

[AW]

Hello,

I am trying to generate a heatmap for specific genes in my single cell dataset but I keep getting a weird error. I have previously generated a heatmap with this code before for the same dataset.

This is my code for average expression:

x <- AverageExpression(x, assays = NULL, return.seurat = TRUE)

I keep getting the error:

Counts matrix provided is not sparse. Creating V5 assay in Seurat Object.
Error in initialize(value, ...) : 
  invalid name for slot of class “Assay5”: check.matrix

Please help

[Ram]

 invalid name for slot of class “Assay5”: check.matrix

Does the error message really have stylized quotes (“...” as opposed to "...")?

[AW]

Yes the message has stylized quotes as in “Assay5”. Can you please help with this?

[Ram]

I haven't used Seurat - I'm sure other users can help you. It's just that it's odd seeing stylized quotes in programming error messages; it means the developer added them on purpose, as most code editors type out simple double quotes.