Problems with cholesky decomposition in pRoloc package
2
@robinkretz-20194
Last seen 5.7 years ago
Germany/Tübingen/NMI
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!
pRoloc
machine learning
cholesky
• 1.6k views
@laurent-gatto-5645
Last seen 10 weeks ago
Belgium
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).
@robinkretz-20194
Last seen 5.7 years ago
Germany/Tübingen/NMI
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
locale:
[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
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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")
.So I installed the latest version and it's working! Thank you very much!
Cheers