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Hello everyone,
I just started to work with MAC and using my own computer (Windows) as a tester.
I am trying to convert a Seurat object to SingleCellExperiment with Convert function of Seurat package. It works in Windows but does not work in MAC.
Also, is there a way in Scater package to read 10X files?
My codes are:
rna.data <- Read10X(data.dir = "C:/Users/hamza/Documents/R/New_Plan/Sample_Data_10X/filtered_gene_bc_matrices/hg19") rna <- CreateSeuratObject(raw.data = rna.data) sce <- Convert(from = rna , to = "sce") keep_feature <- rowSums(counts(sce) > 0) > 0 sce <- sce[keep_feature,]
I use the same codes in MAC but in the "keep_feature" step I have an error which says: 'x' must be an array of at least two dimensions
My session info for MAC:
R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.2 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] scater_1.10.0 SingleCellExperiment_1.4.0 SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.0 matrixStats_0.54.0 [7] Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.0 IRanges_2.16.0 S4Vectors_0.20.0 BiocGenerics_0.28.0 [13] Seurat_2.3.4 Matrix_1.2-15 cowplot_0.9.3 ggplot2_3.1.0 loaded via a namespace (and not attached): [1] ggbeeswarm_0.6.0 Rtsne_0.13 colorspace_1.3-2 class_7.3-14 modeltools_0.2-22 ggridges_0.5.1 mclust_5.4.1 [8] htmlTable_1.12 XVector_0.22.0 base64enc_0.1-3 rstudioapi_0.8 proxy_0.4-22 npsurv_0.4-0 flexmix_2.3-14 [15] bit64_0.9-7 mvtnorm_1.0-8 codetools_0.2-15 splines_3.5.1 R.methodsS3_1.7.1 lsei_1.2-0 robustbase_0.93-3 [22] knitr_1.20 Formula_1.2-3 jsonlite_1.5 ica_1.0-2 cluster_2.0.7-1 kernlab_0.9-27 png_0.1-7 [29] R.oo_1.22.0 HDF5Array_1.10.0 compiler_3.5.1 httr_1.3.1 backports_1.1.2 assertthat_0.2.0 lazyeval_0.2.1 [36] lars_1.2 acepack_1.4.1 htmltools_0.3.6 tools_3.5.1 bindrcpp_0.2.2 igraph_1.2.2 GenomeInfoDbData_1.2.0 [43] gtable_0.2.0 glue_1.3.0 RANN_2.6 reshape2_1.4.3 dplyr_0.7.7 Rcpp_1.0.0 trimcluster_0.1-2.1 [50] gdata_2.18.0 ape_5.2 nlme_3.1-137 DelayedMatrixStats_1.4.0 iterators_1.0.10 fpc_2.1-11.1 gbRd_0.4-11 [57] lmtest_0.9-36 stringr_1.3.1 irlba_2.3.2 gtools_3.8.1 DEoptimR_1.0-8 zlibbioc_1.28.0 MASS_7.3-51.1 [64] zoo_1.8-4 scales_1.0.0 doSNOW_1.0.16 rhdf5_2.26.0 RColorBrewer_1.1-2 yaml_2.2.0 reticulate_1.10 [71] pbapply_1.3-4 gridExtra_2.3 rpart_4.1-13 segmented_0.5-3.0 latticeExtra_0.6-28 stringi_1.2.4 foreach_1.4.4 [78] checkmate_1.8.5 caTools_1.17.1.1 bibtex_0.4.2 Rdpack_0.10-1 SDMTools_1.1-221 rlang_0.3.0.1 pkgconfig_2.0.2 [85] dtw_1.20-1 prabclus_2.2-6 bitops_1.0-6 lattice_0.20-38 Rhdf5lib_1.4.0 ROCR_1.0-7 purrr_0.2.5 [92] bindr_0.1.1 htmlwidgets_1.3 bit_1.1-14 tidyselect_0.2.5 plyr_1.8.4 magrittr_1.5 R6_2.3.0 [99] snow_0.4-3 gplots_3.0.1 Hmisc_4.1-1 pillar_1.3.0 foreign_0.8-71 withr_2.1.2 fitdistrplus_1.0-11 [106] mixtools_1.1.0 RCurl_1.95-4.11 survival_2.43-1 nnet_7.3-12 tibble_1.4.2 tsne_0.1-3 crayon_1.3.4 [113] hdf5r_1.0.1 KernSmooth_2.23-15 viridis_0.5.1 grid_3.5.1 data.table_1.11.8 metap_1.0 digest_0.6.18 [120] diptest_0.75-7 tidyr_0.8.2 R.utils_2.7.0 munsell_0.5.0 beeswarm_0.2.3 viridisLite_0.3.0 vipor_0.4.5
Session info for Windows:
R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=Turkish_Turkey.1254 LC_CTYPE=Turkish_Turkey.1254 [3] LC_MONETARY=Turkish_Turkey.1254 LC_NUMERIC=C [5] LC_TIME=Turkish_Turkey.1254 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] Seurat_2.3.4 Matrix_1.2-14 cowplot_0.9.3 [4] scater_1.10.0 ggplot2_3.1.0 SingleCellExperiment_1.4.0 [7] SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.0 [10] matrixStats_0.54.0 Biobase_2.42.0 GenomicRanges_1.34.0 [13] GenomeInfoDb_1.18.0 IRanges_2.16.0 S4Vectors_0.20.0 [16] BiocGenerics_0.28.0 loaded via a namespace (and not attached): [1] snow_0.4-3 backports_1.1.2 Hmisc_4.1-1 [4] plyr_1.8.4 igraph_1.2.2 lazyeval_0.2.1 [7] splines_3.5.1 digest_0.6.18 foreach_1.4.4 [10] htmltools_0.3.6 viridis_0.5.1 lars_1.2 [13] gdata_2.18.0 magrittr_1.5 checkmate_1.8.5 [16] cluster_2.0.7-1 mixtools_1.1.0 ROCR_1.0-7 [19] R.utils_2.7.0 colorspace_1.3-2 dplyr_0.7.7 [22] crayon_1.3.4 RCurl_1.95-4.11 jsonlite_1.5 [25] bindr_0.1.1 survival_2.43-1 zoo_1.8-4 [28] iterators_1.0.10 ape_5.2 glue_1.3.0 [31] gtable_0.2.0 zlibbioc_1.28.0 XVector_0.22.0 [34] kernlab_0.9-27 Rhdf5lib_1.4.0 prabclus_2.2-6 [37] DEoptimR_1.0-8 HDF5Array_1.10.0 scales_1.0.0 [40] mvtnorm_1.0-8 bibtex_0.4.2 Rcpp_0.12.19 [43] metap_1.0 dtw_1.20-1 viridisLite_0.3.0 [46] htmlTable_1.12 reticulate_1.10 foreign_0.8-71 [49] bit_1.1-14 proxy_0.4-22 mclust_5.4.1 [52] SDMTools_1.1-221 Formula_1.2-3 tsne_0.1-3 [55] htmlwidgets_1.3 httr_1.3.1 gplots_3.0.1 [58] RColorBrewer_1.1-2 fpc_2.1-11.1 acepack_1.4.1 [61] modeltools_0.2-22 ica_1.0-2 pkgconfig_2.0.2 [64] R.methodsS3_1.7.1 flexmix_2.3-14 nnet_7.3-12 [67] tidyselect_0.2.5 rlang_0.3.0.1 reshape2_1.4.3 [70] munsell_0.5.0 tools_3.5.1 ggridges_0.5.1 [73] stringr_1.3.1 yaml_2.2.0 npsurv_0.4-0 [76] knitr_1.20 bit64_0.9-7 fitdistrplus_1.0-11 [79] robustbase_0.93-3 caTools_1.17.1.1 purrr_0.2.5 [82] RANN_2.6 bindrcpp_0.2.2 pbapply_1.3-4 [85] nlme_3.1-137 R.oo_1.22.0 hdf5r_1.0.1 [88] compiler_3.5.1 rstudioapi_0.8 beeswarm_0.2.3 [91] png_0.1-7 lsei_1.2-0 tibble_1.4.2 [94] stringi_1.2.4 lattice_0.20-35 trimcluster_0.1-2.1 [97] pillar_1.3.0 Rdpack_0.10-1 lmtest_0.9-36 [100] data.table_1.11.8 bitops_1.0-6 irlba_2.3.2 [103] gbRd_0.4-11 R6_2.3.0 latticeExtra_0.6-28 [106] KernSmooth_2.23-15 gridExtra_2.3 vipor_0.4.5 [109] codetools_0.2-15 MASS_7.3-50 gtools_3.8.1 [112] assertthat_0.2.0 rhdf5_2.26.0 withr_2.1.2 [115] GenomeInfoDbData_1.2.0 diptest_0.75-7 doSNOW_1.0.16 [118] grid_3.5.1 rpart_4.1-13 tidyr_0.8.2 [121] class_7.3-14 DelayedMatrixStats_1.4.0 segmented_0.5-3.0 [124] Rtsne_0.13 base64enc_0.1-3 ggbeeswarm_0.6.0
Thank you.
Thank you so much. It worked.