I encountered the error when using preprocessQuantile function on RGChannelSet.
mSetSq <- preprocessQuantile(rgSet)
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
Error in base::which(x, arr.ind, useNames, ...) :
argument to 'which' is not logical
Thanks in advance for help.
SessionInfo() of mine is in the following.
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS
Hi,
I encountered the error when using preprocessQuantile function on RGChannelSet. mSetSq <- preprocessQuantile(rgSet) [preprocessQuantile] Mapping to genome. [preprocessQuantile] Fixing outliers. Error in base::which(x, arr.ind, useNames, ...) : argument to 'which' is not logical
Thanks in advance for help.
SessionInfo() of mine is in the following.
R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04 LTS
locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] splines grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] stringr_1.1.0 DMRcate_1.10.2
[3] DMRcatedata_1.10.1 DSS_2.14.0
[5] bsseq_1.10.0 Gviz_1.18.1
[7] minfiData_0.20.0 matrixStats_0.51.0
[9] missMethyl_1.8.0 RColorBrewer_1.1-2
[11] IlluminaHumanMethylation450kmanifest_0.4.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 [13] minfi_1.20.2 bumphunter_1.14.0
[15] locfit_1.5-9.1 iterators_1.0.8
[17] foreach_1.4.3 Biostrings_2.42.1
[19] XVector_0.14.0 SummarizedExperiment_1.4.0
[21] GenomicRanges_1.26.2 GenomeInfoDb_1.10.2
[23] IRanges_2.8.1 S4Vectors_0.12.1
[25] Biobase_2.34.0 BiocGenerics_0.20.0
[27] limma_3.30.7
loaded via a namespace (and not attached): [1] colorspace_1.3-2 siggenes_1.48.0
[3] mclust_5.2.1 biovizBase_1.22.0
[5] htmlTable_1.8 base64enc_0.1-3
[7] dichromat_2.0-0 base64_2.0
[9] interactiveDisplayBase_1.12.0 AnnotationDbi_1.36.0
[11] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 codetools_0.2-15
[13] R.methodsS3_1.7.1 methylumi_2.20.0
[15] knitr_1.15.1 Formula_1.2-1
[17] Rsamtools_1.26.1 annotate_1.52.1
[19] cluster_2.0.5 GO.db_3.4.0
[21] R.oo_1.21.0 shiny_0.14.2
[23] httr_1.2.1 backports_1.0.4
[25] assertthat_0.1 Matrix_1.2-7.1
[27] lazyeval_0.2.0 acepack_1.4.1
[29] htmltools_0.3.5 tools_3.3.2
[31] gtable_0.2.0 doRNG_1.6
[33] Rcpp_0.12.8 multtest_2.30.0
[35] preprocessCore_1.36.0 nlme_3.1-128
[37] rtracklayer_1.34.1 mime_0.5
[39] ensembldb_1.6.2 rngtools_1.2.4
[41] gtools_3.5.0 statmod_1.4.27
[43] XML_3.98-1.5 beanplot_1.2
[45] org.Hs.eg.db_3.4.0 AnnotationHub_2.6.4
[47] zlibbioc_1.20.0 MASS_7.3-45
[49] scales_0.4.1 BSgenome_1.42.0
[51] VariantAnnotation_1.20.2 BiocInstaller_1.24.0
[53] GEOquery_2.40.0 yaml_2.1.14
[55] memoise_1.0.0 gridExtra_2.2.1
[57] ggplot2_2.2.1 pkgmaker_0.22
[59] biomaRt_2.30.0 rpart_4.1-10
[61] reshape_0.8.6 latticeExtra_0.6-28
[63] stringi_1.1.2 RSQLite_1.1-2
[65] genefilter_1.56.0 permute_0.9-4
[67] checkmate_1.8.2 GenomicFeatures_1.26.2
[69] BiocParallel_1.8.1 bitops_1.0-6
[71] nor1mix_1.2-2 lattice_0.20-34
[73] ruv_0.9.6 GenomicAlignments_1.10.0
[75] plyr_1.8.4 magrittr_1.5
[77] R6_2.2.0 Hmisc_4.0-2
[79] DBI_0.5-1 foreign_0.8-67
[81] survival_2.40-1 RCurl_1.95-4.8
[83] nnet_7.3-12 tibble_1.2
[85] data.table_1.10.0 digest_0.6.11
[87] xtable_1.8-2 httpuv_1.3.3
[89] illuminaio_0.16.0 R.utils_2.5.0
[91] openssl_0.9.6 munsell_0.4.3
[93] registry_0.3 BiasedUrn_1.07
[95] quadprog_1.5-5