monocle single cell differential expression: error message for HSMM <- estimateDispersions(HSMM) command
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2.5 years ago

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

single-cell monocle • 2.1k views
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Hello , I encountered the same problem, how did you solve it in the end?

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You need to increase RAM - look for a way to give R more RAM (see this post for example: https://stackoverflow.com/a/1395342/1394178) or seek a machine with higher memory capacity - a node on an HPC or a compute instance on the cloud.

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Hello Ram, Thank you for your reply

my error is that there is a problem with dplyr: my dplyr version is 1.1.2 but I could not install dplyr=0.5.0 or 0.7.0

Warning messages: 1: group_by_() was deprecated in dplyr 0.7.0. Please use group_by() instead. See vignette('programming') for more help The deprecated feature was likely used in the monocle package. Please report the issue to the authors.

enter image description here

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Try creating a new conda environment using miniconda, and install the required version of dplyr in that env.

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My error is that there is a problem with dplyr my dplyr version is 1.1.2 butI can't install dplyr v0.5.0 or v0.7.0 successfully=0.5.0 or 0.7.0

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enter image description here

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those seem like warnings rather than errors

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