dviraran
commented
3 years ago You probably need an older version of Seurat as well. But I would NOT use the old version. It is not maintained there is really no reason to use it. I cannot guarantee that it still works the same as the other packages it is based on were also updated since.
Best, Dvir
Hi @dviraran , I want to use the old SingleR package for analysis,but it get error like below:
this error make me confused, when i run the Seurat(3.2.2) and SingleR(1.0.1) at the same time, the Seurat's DimPlot would be generated below error, how can i fix this question. and it well the old version SingleR using for my data , so i chosen the old version of SingleR.
On this case, how can i fix it from this error?
Any advice would be appreciated.
Best,
hanhuihong
Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] Seurat_3.2.0
loaded via a namespace (and not attached): [1] nlme_3.1-143 bitops_1.0-6 matrixStats_0.57.0
[4] RcppAnnoy_0.0.18 RColorBrewer_1.1-2 httr_1.4.1
[7] sctransform_0.3.1 tools_3.6.0 R6_2.4.1
[10] irlba_2.3.3 rpart_4.1-15 KernSmooth_2.23-16
[13] uwot_0.1.10 mgcv_1.8-31 lazyeval_0.2.2
[16] colorspace_1.4-1 npsurv_0.4-0 tidyselect_1.1.0
[19] gridExtra_2.3 compiler_3.6.0 plotly_4.9.1
[22] caTools_1.17.1.3 scales_1.1.0 lmtest_0.9-37
[25] spatstat.data_1.4-3 ggridges_0.5.1 pbapply_1.4-2
[28] rappdirs_0.3.1 spatstat_1.64-1 goftest_1.2-2
[31] stringr_1.4.0 digest_0.6.25 spatstat.utils_1.17-0 [34] pkgconfig_2.0.3 htmltools_0.5.0 fastmap_1.0.1
[37] htmlwidgets_1.5.1 rlang_0.4.7 shiny_1.5.0
[40] generics_0.0.2 zoo_1.8-6 jsonlite_1.6.1
[43] ica_1.0-2 gtools_3.8.1 dplyr_1.0.2
[46] magrittr_1.5 patchwork_1.0.0 Matrix_1.2-18
[49] Rcpp_1.0.6 munsell_0.5.0 abind_1.4-5
[52] ape_5.3 reticulate_1.14 lifecycle_0.2.0
[55] stringi_1.4.3 MASS_7.3-51.5 gplots_3.0.1.1
[58] Rtsne_0.15 plyr_1.8.5 grid_3.6.0
[61] parallel_3.6.0 gdata_2.18.0 listenv_0.8.0
[64] promises_1.1.0 ggrepel_0.8.1 crayon_1.3.4
[67] deldir_0.1-23 miniUI_0.1.1.1 lattice_0.20-38
[70] cowplot_1.0.0 splines_3.6.0 tensor_1.5
[73] pillar_1.4.3 igraph_1.2.4.2 future.apply_1.3.0
[76] reshape2_1.4.3 codetools_0.2-16 leiden_0.3.1
[79] glue_1.4.0 lsei_1.2-0 data.table_1.12.8
[82] vctrs_0.3.2 png_0.1-7 httpuv_1.5.2
[85] gtable_0.3.0 RANN_2.6.1 purrr_0.3.3
[88] polyclip_1.10-0 tidyr_1.0.0 future_1.15.1
[91] ggplot2_3.3.2 rsvd_1.0.2 mime_0.8
[94] xtable_1.8-4 later_1.0.0 survival_3.1-8
[97] viridisLite_0.3.0 tibble_3.0.3 cluster_2.1.0
[100] globals_0.12.5 fitdistrplus_1.0-14 ellipsis_0.3.0
[103] ROCR_1.0-7