catavallejos
ERROR in no spike-in mode
Hi,
I got errors when I try to run BASiCS_MCMC without spikes. this is the output:
ChainNoSpikes <- BASiCS_MCMC(Data = sce_combine, N = 5000,
+ Thin = 10, Burn = 500,
+ WithSpikes = FALSE, Regression = TRUE,
+ PrintProgress = FALSE,
+ StoreChains=TRUE,
+ RunName="RNAmix_BASiCS_norm")
NAs introduced by coercionRunning no spikes BASiCS sampler (regression case) ...
-----------------------------------------------------
MCMC sampler has been started: 5000 iterations to go.
-----------------------------------------------------
Error when updating delta1414
then the Rstudio crashed. I am using the Rstudio in the linux server, this is the sessionInfo():
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)
Matrix products: default
BLAS: /wehisan/general/system/bioinf-software/bioinfsoftware/R/R-3.5.1/lib64/R/lib/libRblas.so
LAPACK: /wehisan/general/system/bioinf-software/bioinfsoftware/R/R-3.5.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] scran_1.8.2 scater_1.8.0
[3] BASiCS_1.4.0 ggplot2_3.1.0
[5] KernSmooth_2.23-15 SingleCellExperiment_1.4.0
[7] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[9] BiocParallel_1.16.2 matrixStats_0.54.0
[11] Biobase_2.42.0 GenomicRanges_1.34.0
[13] GenomeInfoDb_1.18.1 IRanges_2.16.0
[15] S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 dynamicTreeCut_1.63-1 tools_3.5.1
[4] R6_2.3.0 DT_0.4 HDF5Array_1.8.1
[7] vipor_0.4.5 lazyeval_0.2.1 colorspace_1.4-0
[10] withr_2.1.2 tidyselect_0.2.5 gridExtra_2.3
[13] compiler_3.5.1 scales_1.0.0 stringr_1.3.1
[16] digest_0.6.18 rmarkdown_1.11 XVector_0.22.0
[19] base64enc_0.1-3 pkgconfig_2.0.2 htmltools_0.3.6
[22] limma_3.38.3 htmlwidgets_1.2 rlang_0.3.0.1
[25] FNN_1.1 shiny_1.1.0 DelayedMatrixStats_1.4.0
[28] bindr_0.1.1 jsonlite_1.5 dplyr_0.7.8
[31] RCurl_1.95-4.11 magrittr_1.5 GenomeInfoDbData_1.2.0
[34] Matrix_1.2-14 Rcpp_1.0.0 ggbeeswarm_0.6.0
[37] munsell_0.5.0 Rhdf5lib_1.4.2 viridis_0.5.1
[40] stringi_1.2.3 yaml_2.2.0 edgeR_3.24.2
[43] MASS_7.3-50 zlibbioc_1.28.0 rhdf5_2.24.0
[46] plyr_1.8.4 grid_3.5.1 promises_1.0.1
[49] shinydashboard_0.7.0 lattice_0.20-35 locfit_1.5-9.1
[52] knitr_1.21 pillar_1.2.3 igraph_1.2.1
[55] rjson_0.2.20 reshape2_1.4.3 glue_1.3.0
[58] evaluate_0.12 data.table_1.11.4 httpuv_1.4.4.2
[61] testthat_2.0.1 gtable_0.2.0 purrr_0.2.5
[64] assertthat_0.2.0 xfun_0.4 mime_0.6
[67] xtable_1.8-3 coda_0.19-2 later_0.7.3
[70] viridisLite_0.3.0 tibble_1.4.2 beeswarm_0.2.3
[73] tximport_1.8.0 bindrcpp_0.2.2 statmod_1.4.30
I tried the same code on my Mac laptop and got similar error.
it is noticeable that everytime the number after delta is different in the error message: Error when updating delta1414.
change regression to FALSE does not remove the error.
I am using my benchmark dataset Cellbench. I have tried the BASiCS no spike-in mode early days on the same data without errors. the code is very similar
thank you for your help.
Oh , I am sorry you had this error.
Could you please let me know which version were you running before? (When you had no errors)
Sorry, I didn't keep the record. But I am sure it is in R 3.4 and early 2018.
The spike-in mode works fine though. So I will still use that in my benchmark.
happy new year~
Sorry -- it has been a very busy start of the year, just catching up with some things.
I am unable to replicate the error. Is your data publicly available? If not, could you share it so that I can debug the issue in my computer? Thanks!