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     

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.

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