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Question: SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
1
gravatar for Walter F. Baumann
4 weeks ago by
Walter F. Baumann 10 wrote:

Hi,

I want to get into Single Cell RNA-Seq and found already a good tutorial (https://www.bioconductor.org/help/workflows/simpleSingleCell/). There a package called SingleCellExperiment is introduced. However, the package does not seem to work for me. I had problems with the installation (it always said that it is not available for R version 3.4.2), so I downloaded it and installed it, then it appeared in my package list.

However, the SingleCellExperiment function always returns the following error:

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, "GenomicRanges_OR_GRangesList") is not TRUE

I also tried to reproduce the example on the help page, however, the same error is returned. Here the example:

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))

Below my sessionInfo:

R version 3.4.2 (2017-09-28)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] mgcv_1.8-22                 nlme_3.1-131               
 [3] readxl_1.0.0                R.utils_2.5.0              
 [5] R.oo_1.21.0                 R.methodsS3_1.7.1          
 [7] BiocInstaller_1.26.1        SingleCellExperiment_0.99.4
 [9] SummarizedExperiment_1.6.5  DelayedArray_0.2.7         
[11] matrixStats_0.52.2          Biobase_2.36.2             
[13] GenomicRanges_1.28.6        GenomeInfoDb_1.12.3        
[15] IRanges_2.10.5              S4Vectors_0.14.7           
[17] BiocGenerics_0.22.1         magrittr_1.5               

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13            XVector_0.16.0          zlibbioc_1.22.0        
 [4] lattice_0.20-35         rlang_0.1.2             tools_3.4.2            
 [7] grid_3.4.2              tibble_1.3.4            Matrix_1.2-11          
[10] GenomeInfoDbData_0.99.0 bitops_1.0-6            RCurl_1.95-4.8         
[13] cellranger_1.1.0        compiler_3.4.2     

 

ADD COMMENTlink modified 29 days ago by lahrmannu0 • written 4 weeks ago by Walter F. Baumann 10
1
gravatar for Aaron Lun
4 weeks ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

You're mixing BioC-devel packages (SingleCellExperiment) with BioC-release packages (everything else). If you want to use SingleCellExperiment, you'll need to update to BioC-devel:

library(BiocInstaller)
useDevel()
biocLite()

Packages currently in BioC-devel will become the next BioC-release, which is coming up next month. Workflows are traditionally re-built with BioC-devel packages in preparation for an imminent release.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Aaron Lun17k
0
gravatar for lahrmannu
29 days ago by
lahrmannu0
lahrmannu0 wrote:

Hi there,

because I have exactly the same problem, I'd like to add that it doesn't seem to be a simple "version mix" issue. I have latest linux, latest R and latest bioc devel updates (run: library(BiocInstaller) -> useDevel() -> biocValid() -> biocLite()) (all a couple of minutest old) and the error remains.

Below my sessionInfo:

> sessionInfo()

R version 3.4.2 (2017-09-28)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 16.04.3 LTS

Matrix products: default

BLAS: /usr/lib/libblas/libblas.so.3.6.0

LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:

[1] parallel  stats4    stats     graphics  grDevices utils     datasets

[8] methods   base     

other attached packages:

 [1] SingleCellExperiment_0.99.4 SummarizedExperiment_1.7.10

 [3] DelayedArray_0.3.21         matrixStats_0.52.2         

 [5] Biobase_2.37.2              GenomicRanges_1.29.15      

 [7] GenomeInfoDb_1.13.5         IRanges_2.11.19            

 [9] S4Vectors_0.15.14           BiocGenerics_0.23.4        

[11] BiocInstaller_1.27.6       

loaded via a namespace (and not attached):

 [1] lattice_0.20-35         bitops_1.0-6            grid_3.4.2             

 [4] zlibbioc_1.23.0         XVector_0.17.2          Matrix_1.2-11          

 [7] tools_3.4.2             RCurl_1.95-4.8          compiler_3.4.2         

[10] GenomeInfoDbData_0.99.1

 

ADD COMMENTlink written 29 days ago by lahrmannu0

I must admit that I still cannot reproduce the error. Here is the full set of commands I am running:

library(BiocInstaller)
useDevel() # This fails when devel is already in use.
biocValid(fix=TRUE)
library(SingleCellExperiment)
example(SingleCellExperiment) # this works.

Perhaps you could try re-installing SingleCellExperiment from biocLite? I have a suspicion that the package was built using the old GenomicRanges classes, and probably failed when those class names disappeared in the latest version of the package. If this is the case, there should have been a version bump for SingleCellExperiment - I wonder why that didn't happen.

ADD REPLYlink modified 29 days ago • written 29 days ago by Aaron Lun17k
1

I suggest re-installing the packages that lead from SingleCellExperiment to S4Vectors -- I think SingleCellExperiment, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, and GenomeInfoDb, XVector for good measure.

ADD REPLYlink written 29 days ago by Martin Morgan ♦♦ 20k

Can't tell which one of the packages produced the problem, but re-installing all of the mentioned packages resolved the issue for me - THANKS a lot for the fast help!

ADD REPLYlink written 29 days ago by lahrmannu0
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