Search
Question: Error scatter when creating SingleCellExperiment
0
gravatar for ines.desantiago
23 days ago by
London
ines.desantiago0 wrote:

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              

 

 

 

ADD COMMENTlink modified 23 days ago by Aaron Lun17k • written 23 days ago by ines.desantiago0
0
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 177 users visited in the last hour