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Question: Cannot create SingleCellExperiment object
0
gravatar for Shian Su
3 months ago by
Shian Su10
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Shian Su10 wrote:

 

Using R 3.4.2, BioC 3.6, SingleCellExperiment_1.0.0. The following example code from ?SingleCellExperiment produces an error

 

library(SingleCellExperiment)

ncells <- 100
u <- matrix(rpois(20000, 5), ncol=ncells)
v <- log2(u + 1)

pca <- matrix(runif(ncells*5), ncells)
tsne <- matrix(rnorm(ncells*2), ncells)

sce <- SingleCellExperiment(
  assays = list(counts=u, logcounts=v),
  reducedDims = SimpleList(PCA=pca, tSNE=tsne)
)

 

The error message is

Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “SingleCellExperiment”; is(value, "GenomicRangesORGRangesList") is not TRUE

 

This on a fresh Centos7 VM. If I'm not mistaken these examples are also tested as a part of the build process so I'm very puzzled how the code could fail on me.

EDIT: This appears to work perfectly fine on my MacBook Pro. It may be something strange in the setup of the Unix server I'm on.

ADD COMMENTlink modified 3 months ago by Aaron Lun18k • written 3 months ago by Shian Su10

Can you provide the output of sessionInfo() after library(SingleCellExperiment), and also BiocInstaller::biocValid() ?

ADD REPLYlink written 3 months ago by Martin Morgan ♦♦ 21k
3
gravatar for Aaron Lun
3 months ago by
Aaron Lun18k
Cambridge, United Kingdom
Aaron Lun18k wrote:

Works fine on my machine. Make sure you've properly updated all dependencies, as mentioned in:

C: SingleCellExperiment function in SingleCellExperiment package returns error (whe

ADD COMMENTlink written 3 months ago by Aaron Lun18k

Thanks Aaron, following that other question thread lead me to the solution. I had been drawing most of the BioC packages from a shared location I have no access to. The solution was to use

biocLite("SingleCellExperiment", dependencies=TRUE, lib="~/R/library")

to get a copy of all the dependencies in a local library. This removed the error.

ADD REPLYlink written 3 months ago by Shian Su10
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