Question: Problems with cholesky decomposition in pRoloc package
gravatar for robinkretz
9 days 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 8 days ago • written 9 days ago by robinkretz0
Answer: Problems with cholesky decomposition in pRoloc package
gravatar for Laurent Gatto
9 days 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 9 days ago by Laurent Gatto1.1k
Answer: Problems with cholesky decomposition in pRoloc package
gravatar for robinkretz
8 days 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 8 days 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 7 days ago by Laurent Gatto1.1k

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


ADD REPLYlink written 7 days ago by robinkretz0
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