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AggregateExpression on CITEseq protein data #9648

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yacine902 opened this issue Jan 24, 2025 · 0 comments

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bug

yacine902 commented Jan 24, 2025

When calling AggregateExpression on CITEseq protein data:

bulk.pro <- AggregateExpression(seu, group.by = c("patient"), return.seurat = TRUE, 
normalization.method = 'CLR', margin = 2, assays = "ADT")

I noticed an issue with the normalized data, in that it was CLR normalized with margin = 1 instead of 2:

bulk.pro1 <- AggregateExpression(seu, group.by = c("patient"), return.seurat = TRUE, 
normalization.method = 'CLR', margin = 1, assays = "ADT")
bulk.pro2 <- AggregateExpression(seu, group.by = c("patient"), return.seurat = TRUE, 
normalization.method = 'CLR', margin = 2, assays = "ADT")

all.equal(bulk.pro1[["ADT"]]['data'], bulk.pro2[["ADT"]]['data'])
# return TRUE

Using Seurat_5.0.2

yacine902 added the bug label

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