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Hello! I have a CITE-seq data sample with barcodes, matrix and features files. I load in the barcodes file via Read10X and get the Antibody Capture matrix as a dcgMatrix however I'm a bit stuck on how to reset bounds for the data matrix when making the Elbow Plot
cbmc <- RunPCA(cbmc, verbose = FALSE, npcs = 3)
Warning in irlba(A = t(x = object), nv = npcs, ...) :
You're computing too large a percentage of total singular values, use a standard svd instead.
Warning: No assay specified, setting assay as RNA by default.
ElbowPlot(cbmc, ndims = 50)
Warning: The following arguments are not used: reduction
Error in embeddings[i, j, drop = drop, ...] : subscript out of bounds
In addition: Warning message:
In ElbowPlot(cbmc, ndims = 50) :
The object only has information for 3 reductions
ElbowPlot(cbmc, ndims = 3)
Warning: The following arguments are not used: reduction
Error in embeddings[i, j, drop = drop, ...] : subscript out of bounds
Do I set the bounds within the ElbowPlot function or is this a larger issue within the PCA step? My ultimate goal is to make a ridge plot but I understand the PCA is a necessary feature- could I continue downstream and ignore this error since it seems to be exclusive to the Elbow Plot or will this have impact down the line?
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Hello! I have a CITE-seq data sample with barcodes, matrix and features files. I load in the barcodes file via Read10X and get the Antibody Capture matrix as a dcgMatrix however I'm a bit stuck on how to reset bounds for the data matrix when making the Elbow Plot
Do I set the bounds within the ElbowPlot function or is this a larger issue within the PCA step? My ultimate goal is to make a ridge plot but I understand the PCA is a necessary feature- could I continue downstream and ignore this error since it seems to be exclusive to the Elbow Plot or will this have impact down the line?
Thank you kindly!
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