Question: Problems with cholesky decomposition in pRoloc package
gravatar for robinkretz
10 weeks ago by
robinkretz0 wrote:

Hi, I'm using the pRoloc package to train an TAGM-MCMC model on a proteome data set. For this a Markov Chain Monte Carlo simulation is used via the tagmMcmcTrain() function. However, if I try to run the simulation, an error message occurs:

 > tagm_params <- tagmMcmcTrain(data, fcol = "localization", numIter = 15000, burnin = 4000, thin = 10, numChains = 4)

error: chol(): decomposition failed
Fehler: BiocParallel errors
  element index: 1, 2, 3, 4
  first error: chol(): decomposition failed

I understand, that the problem roots in the covariance matrix not being positive definite. I confirmed this by calculating the eigenvalues of the covariance Matrix. I can correct this by calculating the nearest positive definite covariance matrix by using the nearPD() function. But how can I pass this corrected covariance matrix to the tagmMcmcTrain function?

Thank you very much in advance!

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by robinkretz0
Answer: Problems with cholesky decomposition in pRoloc package
gravatar for Laurent Gatto
10 weeks ago by
Laurent Gatto1.1k
United Kingdom
Laurent Gatto1.1k wrote:

Could you provide the output of sessionInfo please. This was addressed end of last year, which should be available in the latest devel (version 1.23.1).

ADD COMMENTlink written 10 weeks ago by Laurent Gatto1.1k
Answer: Problems with cholesky decomposition in pRoloc package
gravatar for robinkretz
10 weeks ago by
robinkretz0 wrote:

Yes sure, sorry I forgot that.

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
 [1] pRoloc_1.22.1        BiocParallel_1.16.6  MLInterfaces_1.62.0 
 [4] cluster_2.0.7-1      annotate_1.60.1      XML_3.98-1.19       
 [7] AnnotationDbi_1.44.0 IRanges_2.16.0       MSnbase_2.8.3       
[10] ProtGenerics_1.14.0  S4Vectors_0.20.1     mzR_2.16.2          
[13] Rcpp_1.0.0           Biobase_2.42.0       BiocGenerics_0.28.0 

loaded via a namespace (and not attached):
  [1] snow_0.4-3            plyr_1.8.4            igraph_1.2.4         
  [4] lazyeval_0.2.1        splines_3.5.1         ggvis_0.4.4          
  [7] crosstalk_1.0.0       ggplot2_3.1.0         digest_0.6.18        
 [10] foreach_1.4.4         htmltools_0.3.6       viridis_0.5.1        
 [13] gdata_2.18.0          magrittr_1.5          memoise_1.1.0        
 [16] doParallel_1.0.14     mixtools_1.1.0        sfsmisc_1.1-3        
 [19] limma_3.38.3          recipes_0.1.4         gower_0.2.0          
 [22] rda_1.0.2-2.1         lpSolve_5.6.13        prettyunits_1.0.2    
 [25] colorspace_1.4-0      blob_1.1.1            xfun_0.5             
 [28] dplyr_0.8.0.1         crayon_1.3.4          RCurl_1.95-4.12      
 [31] hexbin_1.27.2         genefilter_1.64.0     impute_1.56.0        
 [34] survival_2.42-3       iterators_1.0.10      glue_1.3.0           
 [37] gtable_0.2.0          ipred_0.9-8           zlibbioc_1.28.0      
 [40] kernlab_0.9-27        prabclus_2.2-7        DEoptimR_1.0-8       
 [43] scales_1.0.0          vsn_3.50.0            mvtnorm_1.0-10       
 [46] DBI_1.0.0             viridisLite_0.3.0     xtable_1.8-3         
 [49] progress_1.2.0        bit_1.1-14            proxy_0.4-23         
 [52] mclust_5.4.2          preprocessCore_1.44.0 lava_1.6.5           
 [55] prodlim_2018.04.18    sampling_2.8          htmlwidgets_1.3      
 [58] httr_1.4.0            threejs_0.3.1         FNN_1.1.3            
 [61] RColorBrewer_1.1-2    fpc_2.1-11.1          modeltools_0.2-22    
 [64] pkgconfig_2.0.2       flexmix_2.3-15        nnet_7.3-12          
 [67] caret_6.0-81          tidyselect_0.2.5      rlang_0.3.1          
 [70] reshape2_1.4.3        later_0.8.0           munsell_0.5.0        
 [73] mlbench_2.1-1         tools_3.5.1           LaplacesDemon_16.1.1 
 [76] generics_0.0.2        RSQLite_2.1.1         pls_2.7-0            
 [79] stringr_1.4.0         mzID_1.20.1           ModelMetrics_1.2.2   
 [82] knitr_1.22            bit64_0.9-7           robustbase_0.93-3    
 [85] randomForest_4.6-14   purrr_0.3.1           dendextend_1.9.0     
 [88] ncdf4_1.16.1          nlme_3.1-137          whisker_0.3-2        
 [91] mime_0.6              biomaRt_2.38.0        compiler_3.5.1       
 [94] e1071_1.7-0.1         affyio_1.52.0         tibble_2.0.1         
 [97] stringi_1.3.1         lattice_0.20-35       trimcluster_0.1-2.1  
[100] Matrix_1.2-14         gbm_2.1.5             pillar_1.3.1         
[103] BiocManager_1.30.4    MALDIquant_1.18       data.table_1.12.0    
[106] bitops_1.0-6          httpuv_1.4.5.1        R6_2.4.0             
[109] pcaMethods_1.74.0     affy_1.60.0           hwriter_1.3.2        
[112] promises_1.0.1        gridExtra_2.3         codetools_0.2-15     
[115] MASS_7.3-50           gtools_3.8.1          assertthat_0.2.0     
[118] withr_2.1.2           diptest_0.75-7        hms_0.4.2            
[121] grid_3.5.1            rpart_4.1-13          timeDate_3043.102    
[124] coda_0.19-2           class_7.3-14          segmented_0.5-3.0    
[127] shiny_1.2.0           lubridate_1.7.4       base64enc_0.1-3
ADD COMMENTlink written 10 weeks ago by robinkretz0

Thank you. I will need to check if it was backported correctly - will do that at work this morning. In the meantime, you could try to install the latest version with BiocManager::install("lgatto/pRoloc").

ADD REPLYlink written 10 weeks ago by Laurent Gatto1.1k

So I installed the latest version and it's working! Thank you very much!


ADD REPLYlink written 10 weeks ago by robinkretz0
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