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unable to find an inherited method for function ‘estimateSizeFactors’ for signature ‘"cell_data_set"’ #518

Open jjyotikataria opened 3 years ago

jjyotikataria commented 3 years ago

I ran into the error while pre-processing the data, please let me know how to proceed? @kou @ctrapnell @Loyale @cusanovich @mjsteinbaugh

packageVersion("monocle3") [1] ‘1.0.0’

cds <- load_mm_data(mat_path = "F:/NEW/Projects//filtered_feature_bc_matrix/outs/filtered_gene_bc_matrices/hg19/matrix.mtx.gz",

cds class: cell_data_set dim: 36601 1735 metadata(1): cds_version assays(1): counts rownames(36601): ENSG00000243485 ENSG00000237613 ... ENSG00000278817 ENSG00000277196 rowData names(2): V2 V3 colnames(1735): AAACCCACAGGCCCTA-1 AAACCCATCATGAAAG-1 ... TTTGGAGTCTTGGTGA-1 TTTGTTGTCATTCTTG-1 colData names(3): cell Size_Factor n.umi reducedDimNames(0): mainExpName: NULL altExpNames(0):

DelayedArray:::set_verbose_block_processing(TRUE) [1] FALSE options(DelayedArray.block.size=1000e6) cds <- estimateSizeFactors(cds) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘estimateSizeFactors’ for signature ‘"cell_data_set"’

mjsteinbaugh commented 3 years ago

@jjyotikataria Do you run into the same issue when using the bioconda recipe of r-monocle3?

The easiest way to check is using the Docker image:

image='quay.io/biocontainers/r-monocle3:1.0.0--r41h7d875b9_1'
docker pull "$image"
docker run -it "$image"
R
library(monocle3)

I'm checking my local install of monocle3 on R 4.1.0 / Bioconductor 3.13 to see if I can reproduce this issue.

mjsteinbaugh commented 3 years ago

This minimal working example is currently working for me with the latest monocle3 code from GitHub. Hope that helps!