scater runUMAP
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@a9c5eb20
Last seen 4 months ago
United States

Hello,

I got the warning message:
In .check_reddim_names(x, value, withDimnames) :
non-NULL 'rownames(value)' should be the same as
'colnames(x)' for 'reducedDim<-'. This will be an error
in the next release of Bioconductor.

Does anyone have solutions?

# package version: scran-1.22.1, scuttle-1.4.0, scater-1.22.0 
library(scran); library(scuttle)                                                                                                   
sce <- mockSCE(); sce <- logNormCounts(sce)                                                                                                          
colnames(sce) <- c(rep('cell1', 100), rep('cell2', 100))                                                                                                                                                                                                             
# Modelling the variance:                                                                                                          
var.stats <- modelGeneVar(sce)                                                                                                                                                                                                                                      
# Automatically storing the results.                                                                                               
sce <- denoisePCA(sce, technical=var.stats, subset.row=rownames(var.stats))                                                        

library(scater)                                                                                                                    
sce <- runUMAP(sce, dimred="PCA")

Regards

scater runUMAP • 647 views
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Peter Hickey ▴ 630
@petehaitch
Last seen 25 days ago
Walter and Eliza Hall Institute of Mediā€¦

Why are you doing colnames(sce) <- c(rep('cell1', 100), rep('cell2', 100))? It's generally a bad idea for different columns (cells) to have the same name, and this is what is raising this warning. If instead you use unique colnames, e.g., something like colnames(sce) <- paste0("cell", seq_len(ncol(sce))), then you won't have any problem.

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Yes, in my work I need to use duplicated column names.

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Without knowing why you need that, I'd still strongly recommend using unique column names and just store the duplicate-containing cell-level metadata in colData(sce) for when you need to access it (e.g., sce$alt_colnames <- (rep('cell1', 100), rep('cell2', 100)))

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Got it. Thank you!

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