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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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one node produced an error: Error in ED2(data) #103

Open eshraaqsaeed opened 3 years ago

eshraaqsaeed commented 3 years ago

On running sc3 function, this error appears: Error in checkForRemoteErrors(val) : one node produced an error: Error in ED2(data) : Not compatible with requested type: [type=list; target=double].

Code: (sce object on Yan dataset) sce <- sc3(sce, ks = 6, biology = TRUE)

Session Info: R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8.1 x64 (build 9600)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] scater_1.16.2 ggplot2_3.3.2 SC3_1.18.0
[4] SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2 DelayedArray_0.14.1
[7] matrixStats_0.56.0 Biobase_2.48.0 GenomicRanges_1.40.0
[10] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[13] BiocGenerics_0.34.0

loaded via a namespace (and not attached): [1] viridis_0.5.1 BiocSingular_1.4.0 viridisLite_0.3.0
[4] foreach_1.5.0 DelayedMatrixStats_1.10.1 shiny_1.5.0
[7] doRNG_1.8.2 GenomeInfoDbData_1.2.3 vipor_0.4.5
[10] robustbase_0.93-6 pillar_1.4.7 lattice_0.20-41
[13] glue_1.4.2 digest_0.6.27 RColorBrewer_1.1-2
[16] promises_1.1.1 XVector_0.28.0 colorspace_1.4-1
[19] cowplot_1.0.0 htmltools_0.5.1.1 httpuv_1.5.4
[22] Matrix_1.3-2 pcaPP_1.9-73 WriteXLS_6.2.0
[25] pkgconfig_2.0.3 pheatmap_1.0.12 zlibbioc_1.34.0
[28] purrr_0.3.4 xtable_1.8-4 mvtnorm_1.1-1
[31] scales_1.1.1 later_1.1.0.1 BiocParallel_1.22.0
[34] tibble_3.0.3 farver_2.0.3 generics_0.0.2
[37] ellipsis_0.3.1 withr_2.3.0 ROCR_1.0-11
[40] magrittr_2.0.1 crayon_1.3.4 mime_0.9
[43] doParallel_1.0.15 class_7.3-18 beeswarm_0.2.3
[46] tools_4.0.4 lifecycle_0.2.0 munsell_0.5.0
[49] cluster_2.1.0 rngtools_1.5 irlba_2.3.3
[52] compiler_4.0.4 e1071_1.7-4 rsvd_1.0.3
[55] tinytex_0.25 rlang_0.4.10 grid_4.0.4
[58] RCurl_1.98-1.2 iterators_1.0.12 BiocNeighbors_1.6.0
[61] rstudioapi_0.13 labeling_0.4.2 bitops_1.0-6
[64] gtable_0.3.0 codetools_0.2-18 rrcov_1.5-5
[67] R6_2.5.0 gridExtra_2.3 dplyr_1.0.1
[70] fastmap_1.0.1 ggbeeswarm_0.6.0 Rcpp_1.0.6
[73] vctrs_0.3.2 DEoptimR_1.0-8 tidyselect_1.1.0
[76] xfun_0.16

**Additional Comment: I restarted a new R session and the problem still existed.

Thank you in advance

boyiguo1 commented 1 year ago

This previous issue seems relevant: https://github.com/hemberg-lab/SC3/issues/53#issuecomment-355736905 TLDR: you may want to see what is the data structure that contains your count/log count data. They should be matrix.