Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
Entering edit mode
Lucky • 0
Last seen 8 months ago

Hello I am trying to add my data to class SingleCellExperiment while doing so getting an error, When am trying add metadata info please help me is it a bug or I am doing anything wrong even though i have same number names as columns still getting a error

Thank you

tpm_count <- read.table("TPM.tsv", sep="\t", header=T, row.names=1)
[1] 24285   179

meta<-read.table("Cell_info.tsv", header=T, sep="\t")
[1] 179   3

cell.labels <- meta$Stage2

[1] 179

sce <- SummarizedExperiment(
  assays = list(counts = as.matrix(tpm_count), colData=DataFrame(label=cell.labels)

**Error in method(object) : all assays must have the same nrow and ncol**

sessionInfo( )

R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/

 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8     LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8   
 [7] LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RColorBrewer_1.1-3          circlize_0.4.14             ComplexHeatmap_2.8.0        scater_1.20.1               ggplot2_3.3.5               umap_0.2.8.0               
 [7] magrittr_2.0.3              dplyr_1.0.8                 scran_1.20.1                scuttle_1.2.1               SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0
[13] Biobase_2.52.0              GenomicRanges_1.44.0        GenomeInfoDb_1.28.4         IRanges_2.26.0              S4Vectors_0.30.2            BiocGenerics_0.38.0        
[19] MatrixGenerics_1.4.3        matrixStats_0.61.0         

loaded via a namespace (and not attached):
 [1] bitops_1.0-7              doParallel_1.0.17         tools_4.1.3               utf8_1.2.2                R6_2.5.1                  irlba_2.3.5               vipor_0.4.5              
 [8] DBI_1.1.2                 colorspace_2.0-3          GetoptLong_1.0.5          withr_2.5.0               tidyselect_1.1.2          gridExtra_2.3             compiler_4.1.3           
[15] cli_3.2.0                 BiocNeighbors_1.10.0      Cairo_1.5-15              DelayedArray_0.18.0       scales_1.1.1              askpass_1.1               digest_0.6.29            
[22] XVector_0.32.0            pkgconfig_2.0.3           sparseMatrixStats_1.4.2   limma_3.48.3              rlang_1.0.2               GlobalOptions_0.1.2       DelayedMatrixStats_1.14.3
[29] shape_1.4.6               generics_0.1.2            jsonlite_1.8.0            BiocParallel_1.26.2       RCurl_1.98-1.6            BiocSingular_1.8.1        GenomeInfoDbData_1.2.6   
[36] Matrix_1.4-1              Rcpp_1.0.8.3              ggbeeswarm_0.6.0          munsell_0.5.0             fansi_1.0.3               reticulate_1.24           viridis_0.6.2            
[43] lifecycle_1.0.1           edgeR_3.34.1              zlibbioc_1.38.0           dqrng_0.3.0               crayon_1.5.1              lattice_0.20-45           beachmat_2.8.1           
[50] locfit_1.5-9.5            metapod_1.0.0             pillar_1.7.0              igraph_1.3.0              rjson_0.2.21              codetools_0.2-18          ScaledMatrix_1.0.0       
[57] glue_1.6.2                png_0.1-7                 vctrs_0.4.0               foreach_1.5.2             gtable_0.3.0              openssl_2.0.0             purrr_0.3.4              
[64] clue_0.3-60               assertthat_0.2.1          rsvd_1.0.5                RSpectra_0.16-0           viridisLite_0.4.0         tibble_3.1.6              iterators_1.0.14         
[71] beeswarm_0.4.0            cluster_2.1.2             bluster_1.2.1             statmod_1.4.36            ellipsis_0.3.2
SingleCellExperiment scran scater • 378 views
Entering edit mode
Basti ▴ 530
Last seen 1 day ago

Pay attention to your parenthesis, your arguments are not correct, it should be :

sce <- SummarizedExperiment(
  assays = list(counts = as.matrix(tpm_count)), colData=DataFrame(label=cell.labels)

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