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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)
dim(tpm_count)
[1] 24285 179
meta<-read.table("Cell_info.tsv", header=T, sep="\t")
dim(meta)
[1] 179 3
cell.labels <- meta$Stage2
length(cell.labels)
[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/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
locale:
[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