Entering edit mode
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
Hi, I know it has been some years since this problem occurred with you, but I have ran into the same problem with several datasets known to work as well. So I was wondering whether there is a fix for this problem? Best, Peter Brederlow