Question: Error scatter when creating SingleCellExperiment
gravatar for ines.desantiago
23 days ago by
ines.desantiago0 wrote:


 have the following error (see below) and no clue on how to solve this. I attached the R-Data object this post..




> 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



[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              




ADD COMMENTlink modified 23 days ago by Aaron Lun17k • written 23 days ago by ines.desantiago0
gravatar for Aaron Lun
23 days ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

See SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example) and reinstall SingleCellExperiment.

ADD COMMENTlink written 23 days ago by Aaron Lun17k
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