Problems with cholesky decomposition in pRoloc package
2
@robinkretz-20194
Last seen 5.6 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 2 days 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 5.6 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