hi
have the following error (see below) and no clue on how to solve this. I attached the R-Data object this post..
https://www.dropbox.com/s/vuqh2rkqgltyhvy/datatotestscater.RData?dl=0
> load("datatotestscater.RData")
> sce_out <- SingleCellExperiment(
+ list(exprs = log2(tpm + logExprsOffset),
+ counts = est_counts, tpm = tpm,
+ feature_effective_length = feat_eff_len),
+ colData = pdata, rowData = fdata)
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
>
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] scater_1.5.21 SingleCellExperiment_0.99.4
[3] SummarizedExperiment_1.7.10 DelayedArray_0.3.21
[5] matrixStats_0.52.2 GenomicRanges_1.29.15
[7] GenomeInfoDb_1.13.5 IRanges_2.11.19
[9] S4Vectors_0.15.14 ggplot2_2.2.1
[11] Biobase_2.37.2 BiocGenerics_0.23.4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 locfit_1.5-9.1 lattice_0.20-35
[4] prettyunits_1.0.2 assertthat_0.2.0 digest_0.6.12
[7] mime_0.5 R6_2.2.2 plyr_1.8.4
[10] RSQLite_2.0 zlibbioc_1.23.0 rlang_0.1.2
[13] progress_1.1.2 lazyeval_0.2.0 data.table_1.10.4-2
[16] blob_1.1.0 Matrix_1.2-11 stringr_1.2.0
[19] RCurl_1.95-4.8 bit_1.1-12 biomaRt_2.33.4
[22] munsell_0.4.3 shiny_1.0.5 compiler_3.4.2
[25] httpuv_1.3.5 vipor_0.4.5 pkgconfig_2.0.1
[28] ggbeeswarm_0.6.0 htmltools_0.3.6 tximport_1.5.1
[31] tibble_1.3.4 gridExtra_2.3 GenomeInfoDbData_0.99.0
[34] edgeR_3.19.8 XML_3.98-1.9 viridisLite_0.2.0
[37] dplyr_0.7.4 bitops_1.0-6 grid_3.4.2
[40] xtable_1.8-2 gtable_0.2.0 DBI_0.7
[43] magrittr_1.5 scales_0.5.0 stringi_1.1.5
[46] XVector_0.17.2 reshape2_1.4.2 viridis_0.4.0
[49] bindrcpp_0.2 limma_3.33.14 rjson_0.2.15
[52] tools_3.4.2 bit64_0.9-7 glue_1.1.1
[55] beeswarm_0.2.3 rhdf5_2.21.6 AnnotationDbi_1.39.4
[58] colorspace_1.3-2 shinydashboard_0.6.1 memoise_1.1.0
[61] bindr_0.1
>
