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:
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:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats4 stats graphics grDevices utils datasets  methods base other attached packages:  mgcv_1.8-22 nlme_3.1-131  readxl_1.0.0 R.utils_2.5.0  R.oo_1.21.0 R.methodsS3_1.7.1  BiocInstaller_1.26.1 SingleCellExperiment_0.99.4  SummarizedExperiment_1.6.5 DelayedArray_0.2.7  matrixStats_0.52.2 Biobase_2.36.2  GenomicRanges_1.28.6 GenomeInfoDb_1.12.3  IRanges_2.10.5 S4Vectors_0.14.7  BiocGenerics_0.22.1 magrittr_1.5 loaded via a namespace (and not attached):  Rcpp_0.12.13 XVector_0.16.0 zlibbioc_1.22.0  lattice_0.20-35 rlang_0.1.2 tools_3.4.2  grid_3.4.2 tibble_1.3.4 Matrix_1.2-11  GenomeInfoDbData_0.99.0 bitops_1.0-6 RCurl_1.95-4.8  cellranger_1.1.0 compiler_3.4.2