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cds = new_cell_data_set(expression_matrix,
cell_metadata = cell_metadata,
gene_metadata = gene_annotation)
cds <- preprocess_cds(cds, num_dim = 50) # I am getting error at this point
The text was updated successfully, but these errors were encountered:
HI,
I am trying to use monocle on the sample data provided by "https://cole-trapnell-lab.github.io/monocle3/docs/clustering/".
However, at "cds <- preprocess_cds(cds, num_dim = 100)" I am getting the following error.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘colVars’ for signature ‘"dgCMatrix"’
My codes are:
library(monocle3)
library(dplyr) # imported for some downstream data manipulation
library(Matrix)
expression_matrix <- readRDS(url("http://staff.washington.edu/hpliner/data/cao_l2_expression.rds"))
cell_metadata <- readRDS(url("http://staff.washington.edu/hpliner/data/cao_l2_colData.rds"))
gene_annotation <- readRDS(url("http://staff.washington.edu/hpliner/data/cao_l2_rowData.rds"))
cds = new_cell_data_set(expression_matrix,
cell_metadata = cell_metadata,
gene_metadata = gene_annotation)
cds <- preprocess_cds(cds, num_dim = 50) # I am getting error at this point
The text was updated successfully, but these errors were encountered: