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I tried to run fastMNN (installed today from bioconductor), but I get more cells than expecte din the corrected object. Any idea why?
sobj <- subset(data, features=hvg) print('sobj') print(sobj) expr <- GetAssayData(object = sobj ,slot = "data") print('expr') print(dim(expr)) sce <- fastMNN(expr, batch = sobj@meta.data[[batch]]) print('sce') print(dim(sce)) [1] "sobj" An object of class Seurat 2000 features across 2730 samples within 1 assay Active assay: originalexp (2000 features, 0 variable features) [1] "expr" [1] 2000 2730 [1] "sce" [1] 2000 9815
The text was updated successfully, but these errors were encountered:
I have no idea. I assume that expr is a matrix or dgCMatrix, and not some custom class that might be reinterpreted as a list.
expr
dgCMatrix
Sorry, something went wrong.
Yes, it is a matrix
class(expr) 'matrix''array'
Well, I dunno. Works fine for me on batchelor 1.10.0.
library(batchelor) x <- matrix(runif(2000000), ncol=1000) dim(x) ## [1] 2000 1000 batch <- sample(2, ncol(x), replace=TRUE) out <- fastMNN(x, batch=batch) dim(out) ## [1] 2000 1000
Try modifying the example above to reproduce the error.
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I tried to run fastMNN (installed today from bioconductor), but I get more cells than expecte din the corrected object. Any idea why?
The text was updated successfully, but these errors were encountered: