Hi,

I'm trying to perform single cell differential gene expression using a public dataset.

I'm working through this monocle workflow: https://bioconductor.statistik.tu-dortmund.de/packages/3.5/bioc/vignettes/monocle/inst/doc/monocle-vignette.pdf.

These are the commands I've used:

library(Matrix)
mat <- Matrix::readMM("~/Downloads/GSM4952363_OS_1_matrix.mtx.gz")
features <- read.delim("~/Downloads/GSM4952363_OS_1_features.tsv.gz",
                        header=FALSE)
barcodes <- read.delim("~/Downloads/GSM4952363_OS_1_barcodes.tsv.gz",
                        header=FALSE)
library(monocle)
colnames(features)[2] <- "gene_short_name"

pd <- new("AnnotatedDataFrame", data = barcodes)
 fd <- new("AnnotatedDataFrame", data = features)

HSMM <- newCellDataSet(as(mat, "sparseMatrix"),
                phenoData = pd,
                featureData = fd,
                lowerDetectionLimit = 0.5,
                expressionFamily = negbinomial.size())
HSMM <- estimateSizeFactors(HSMM)

However I get the following error message for this command: HSMM <- estimateDispersions(HSMM)

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'rowMeans': vector memory exhausted (limit reached?)
In addition: Warning messages:
1: `group_by_()` was deprecated in dplyr 0.7.0.
Please use `group_by()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. 
2: `select_()` was deprecated in dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

I also get this error message for HSMM <- estimateDispersions(HSMM):

Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'rowMeans': vector memory exhausted (limit reached?)

Does anyone know how I might correct this?

Thank you