PSEUDOBULK HELP-DE Expression in scRNA-seq

Question

[bioinformatics.girl]

I have been trying for days to get my pseudobulk code to work, this is the current code snippet:

#rna$SampleIDs<-rownames([e-mail])

rna<-NormalizeData(rna)
rna<-FindVariableFeatures(rna)
rna<-ScaleData(rna)
rna<-RunPCA(rna)

##### Aggregate counts across the cells at the sample level.
cts<-AggregateExpression(rna, 
                         group.by = "cellClass", "SampleIDs",
                         assays='RNA',
                         slot="counts",
                         return.seurat=FALSE,
                         verbose=TRUE
)

Error is:
Warning: The following 1 features were not found in the RNA assay: SampleIDs
Warning: None of the features specified were found in the RNA assay.

I re-scaled and normalized everything thinking this would work, and the issue persists. Any pointers, please?

Answer 1

[jv]

You need to concatenate your group.by strings:

cts<-AggregateExpression(rna, 
                         group.by = c("cellClass", "SampleIDs"),
                         assays='RNA',
                         slot="counts",
                         return.seurat=FALSE,
                         verbose=TRUE

[bioinformatics.girl]

Why of course. I thank you so much for your help!

[jv]

if the solution fixed your issue, please accept the answer and up-vote