ERROR in no spike-in mode

[LuyiTian]

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.

[catavallejos]

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)

[LuyiTian]

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~

[catavallejos]

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!