Question: ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all numeric variables"
0
gravatar for moldach
5 months ago by
moldach20
Canada/Montreal/Douglas Mental Health Institute
moldach20 wrote:

We've ran into a problem where ChAMP::champ.norm() has all of a sudden stopped working for our users. We've ran it again on datasets which have worked previously (on both dfs and matrices) and were getting the same error:

test_betas <- data.frame(slide1 = c(0.83930246, 0.81656241, 0.88592212, 0.77763971, 0.84525827, 0.74552572, 0.87266718, 0.81861486, 0.88888392, 0.90252657), slide2 = c(0.89440246, 0.91509237, 0.91008524, 0.73117381, 0.89273372, 0.91529722, 0.90761344, 0.73750841, 0.92563172, 0.9437351), slide3 = c(0.83930246, 0.81656241, 0.88592212, 0.77763971, 0.84525827, 0.74552572, 0.87266718, 0.81861486, 0.88888392, 0.90252657))

beta_matrix=as.matrix(test_betas)

forDNAm = ChAMP::champ.norm(beta = beta_matrix, cores = 18)

Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x],  : 
  task 1 failed - "cannot take a sample larger than the population when 'replace = FALSE'"

Here's a look at sessionInfo():

R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/apps/anaconda2/lib/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] cowplot_0.9.4                              here_0.1                                   data.table_1.12.2                         
 [4] forcats_0.4.0                              stringr_1.4.0                              dplyr_0.8.0.1                             
 [7] purrr_0.3.2                                tidyr_0.8.3                                tibble_2.1.1                              
[10] ggplot2_3.1.1                              tidyverse_1.2.1                            readr_1.3.1                               
[13] ChAMP_2.12.4                               IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.18.0        
[16] DMRcate_1.18.0                             DMRcatedata_1.18.0                         DSS_2.30.1                                
[19] bsseq_1.18.0                               FEM_3.10.0                                 graph_1.60.0                              
[22] org.Hs.eg.db_3.7.0                         impute_1.56.0                              igraph_1.2.4.1                            
[25] corrplot_0.84                              marray_1.60.0                              limma_3.38.3                              
[28] Matrix_1.2-17                              AnnotationDbi_1.44.0                       ChAMPdata_2.14.1                          
[31] minfi_1.28.4                               bumphunter_1.24.5                          locfit_1.5-9.1                            
[34] iterators_1.0.10                           foreach_1.4.4                              Biostrings_2.50.2                         
[37] XVector_0.22.0                             SummarizedExperiment_1.12.0                DelayedArray_0.8.0                        
[40] BiocParallel_1.16.6                        matrixStats_0.54.0                         Biobase_2.42.0                            
[43] GenomicRanges_1.34.0                       GenomeInfoDb_1.18.2                        IRanges_2.16.0                            
[46] S4Vectors_0.20.1                           BiocGenerics_0.28.0                        usethis_1.5.0                             
[49] devtools_2.0.2                            

loaded via a namespace (and not attached):
  [1] lookup_0.0.0.9000                                   rtracklayer_1.42.2                                 
  [3] prabclus_2.2-7                                      R.methodsS3_1.7.1                                  
  [5] wateRmelon_1.26.0                                   pkgmaker_0.27                                      
  [7] acepack_1.4.1                                       bit64_0.9-7                                        
  [9] knitr_1.22                                          R.utils_2.8.0                                      
 [11] rpart_4.1-15                                        generics_0.0.2                                     
 [13] RCurl_1.95-4.12                                     GEOquery_2.50.5                                    
 [15] AnnotationFilter_1.6.0                              doParallel_1.0.14                                  
 [17] GenomicFeatures_1.34.8                              preprocessCore_1.44.0                              
 [19] callr_3.2.0                                         RSQLite_2.1.1                                      
 [21] combinat_0.0-8                                      bit_1.1-14                                         
 [23] lubridate_1.7.4                                     xml2_1.2.0                                         
 [25] httpuv_1.5.1                                        assertthat_0.2.1                                   
 [27] IlluminaHumanMethylation450kmanifest_0.4.0          viridis_0.5.1                                      
 [29] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 isva_1.9                                           
 [31] xfun_0.6                                            hms_0.4.2                                          
 [33] evaluate_0.13                                       missMethyl_1.16.0                                  
 [35] DNAcopy_1.56.0                                      promises_1.0.1                                     
 [37] DEoptimR_1.0-8                                      progress_1.2.0                                     
 [39] readxl_1.3.1                                        dendextend_1.10.0                                  
 [41] DBI_1.0.0                                           htmlwidgets_1.3                                    
 [43] reshape_0.8.8                                       ROC_1.58.0                                         
 [45] backports_1.1.4                                     trimcluster_0.1-2.1                                
 [47] permute_0.9-5                                       annotate_1.60.1                                    
 [49] biomaRt_2.38.0                                      remotes_2.0.4                                      
 [51] ensembldb_2.6.8                                     withr_2.1.2                                        
 [53] packrat_0.5.0                                       globaltest_5.36.0                                  
 [55] Gviz_1.26.5                                         robustbase_0.93-4                                  
 [57] BSgenome_1.50.0                                     checkmate_1.9.1                                    
 [59] GenomicAlignments_1.18.1                            prettyunits_1.0.2                                  
 [61] mclust_5.4.3                                        cluster_2.0.8                                      
 [63] RPMM_1.25                                           lazyeval_0.2.2                                     
 [65] crayon_1.3.4                                        genefilter_1.64.0                                  
 [67] pkgconfig_2.0.2                                     nlme_3.1-139                                       
 [69] pkgload_1.0.2                                       ProtGenerics_1.14.0                                
 [71] nnet_7.3-12                                         diptest_0.75-7                                     
 [73] rlang_0.3.4                                         nleqslv_3.3.2                                      
 [75] registry_0.5-1                                      affyio_1.52.0                                      
 [77] modelr_0.1.4                                        dichromat_2.0-0                                    
 [79] cellranger_1.1.0                                    rprojroot_1.3-2                                    
 [81] rngtools_1.3.1                                      IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
 [83] base64_2.0                                          Rhdf5lib_1.4.3                                     
 [85] base64enc_0.1-3                                     geneLenDataBase_1.18.0                             
 [87] whisker_0.3-2                                       processx_3.3.0                                     
 [89] viridisLite_0.3.0                                   bitops_1.0-6                                       
 [91] R.oo_1.22.0                                         KernSmooth_2.23-15                                 
 [93] blob_1.1.1                                          DelayedMatrixStats_1.4.0                           
 [95] doRNG_1.7.1                                         qvalue_2.14.1                                      
 [97] nor1mix_1.2-3                                       scales_1.0.0                                       
 [99] memoise_1.1.0.9000                                  magrittr_1.5                                       
[101] plyr_1.8.4                                          bibtex_0.4.2                                       
[103] zlibbioc_1.28.0                                     compiler_3.5.3                                     
[105] RColorBrewer_1.1-2                                  illuminaio_0.24.0                                  
[107] clue_0.3-57                                         Rsamtools_1.34.1                                   
[109] cli_1.1.0                                           affy_1.60.0                                        
[111] JADE_2.0-1                                          IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[113] ps_1.3.0                                            htmlTable_1.13.1                                   
[115] Formula_1.2-3                                       MASS_7.3-51.3                                      
[117] mgcv_1.8-28                                         tidyselect_0.2.5                                   
[119] stringi_1.4.3                                       askpass_1.1                                        
[121] latticeExtra_0.6-28                                 grid_3.5.3                                         
[123] VariantAnnotation_1.28.13                           tools_3.5.3                                        
[125] ruv_0.9.7                                           rstudioapi_0.10                                    
[127] foreign_0.8-71                                      gridExtra_2.3                                      
[129] digest_0.6.18                                       BiocManager_1.30.4                                 
[131] shiny_1.3.2                                         fpc_2.1-11.1                                       
[133] quadprog_1.5-5                                      Rcpp_1.0.1                                         
[135] broom_0.5.2                                         siggenes_1.56.0                                    
[137] later_0.8.0                                         httr_1.4.0                                         
[139] biovizBase_1.30.1                                   lumi_2.34.0                                        
[141] kernlab_0.9-27                                      colorspace_1.4-1                                   
[143] rvest_0.3.3                                         XML_3.98-1.19                                      
[145] fs_1.2.7                                            statmod_1.4.30                                     
[147] kpmt_0.1.0                                          multtest_2.38.0                                    
[149] flexmix_2.3-15                                      shinythemes_1.1.2                                  
[151] plotly_4.9.0                                        sessioninfo_1.1.1                                  
[153] xtable_1.8-4                                        jsonlite_1.6                                       
[155] modeltools_0.2-22                                   testthat_2.1.1                                     
[157] R6_2.4.0                                            Hmisc_4.2-0                                        
[159] pillar_1.3.1                                        htmltools_0.3.6                                    
[161] mime_0.6                                            glue_1.3.1                                         
[163] class_7.3-15                                        beanplot_1.2                                       
[165] codetools_0.2-16                                    mvtnorm_1.0-10                                     
[167] pkgbuild_1.0.3                                      lattice_0.20-38                                    
[169] sva_3.30.1                                          highlite_0.0.0.9000                                
[171] curl_3.3                                            BiasedUrn_1.07                                     
[173] gtools_3.8.1                                        GO.db_3.7.0                                        
[175] openssl_1.3                                         survival_2.44-1.1                                  
[177] rmarkdown_1.12                                      methylumi_2.28.0                                   
[179] desc_1.2.0                                          fastICA_1.2-1                                      
[181] munsell_0.5.0                                       rhdf5_2.26.2                                       
[183] GenomeInfoDbData_1.2.0                              goseq_1.34.1                                       
[185] HDF5Array_1.10.1                                    haven_2.1.0                                        
[187] reshape2_1.4.3                                      gtable_0.3.0    
champ methylation bmiq • 163 views
ADD COMMENTlink modified 5 months ago by Yuan Tian120 • written 5 months ago by moldach20
Answer: ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(b
0
gravatar for Yuan Tian
5 months ago by
Yuan Tian120
University College London
Yuan Tian120 wrote:

Um...This is the second time I receive this error report this week. But I have never seen this error before, and no one reported before this week. I suspect the reason is some functions or packages ChAMP relies on are just updated, which caused some problem inside. I will have a look this week, and fix it.

Best Yuan Tian

ADD COMMENTlink written 5 months ago by Yuan Tian120
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