Error generating normalized MethylSet from RGChannelSet #282
Description
I'm working with a set of DNA methylation data from dried blood spots. These data are from the EPIC V2 chip and annotated with 20a1.hg38. I've successfully read in the IDATs and created an RGChannelSet. However, when I try to run the normalization function preprocessNoob(), I get the error below:
> #'Run Noob preprocessing on rgset
> Mset <- preprocessNoob(RGset)
Error in if (s == 0) stop("cannot estimate scale: MAD is zero for this sample") :
missing value where TRUE/FALSE needed
My RGset seems to be loaded correctly:
> RGset
class: RGChannelSetExtended
dim: 1105209 35
metadata(0):
assays(5): Green Red GreenSD RedSD NBeads
rownames(1105209): 1600157 1600179 ... 99810982
99810990
rowData names(0):
colnames(35): GSM8598217_207218130019_R02C01
GSM8598220_207218130019_R05C01 ...
GSM8598355_207714930042_R07C01
GSM8598361_207714930137_R02C01
colData names(9): Sample_Name title ... Basename
filenames
Annotation
array: IlluminaHumanMethylationEPICv2
annotation: 20a1.hg38
Could you please help me troubleshoot this?
I saw another open issue from Sep 2024 that noted the same issue with EPIC V2 data.
Thank you in advance!
sessionInfo():
> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] grid parallel stats4 stats graphics
[6] grDevices utils datasets methods base
other attached packages:
[1] IlluminaHumanMethylationEPICv2manifest_0.1.0
[2] IlluminaHumanMethylationEPICv2anno.20a1.hg38_1.0.0
[3] MethylCIBERSORT_0.2.1
[4] GEOquery_2.72.0
[5] conumee2_2.1
[6] nullranges_1.10.0
[7] RnBeads_2.22.0
[8] plyr_1.8.9
[9] methylumi_2.50.0
[10] FDb.InfiniumMethylation.hg19_2.2.0
[11] org.Hs.eg.db_3.19.1
[12] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[13] GenomicFeatures_1.56.0
[14] AnnotationDbi_1.66.0
[15] reshape2_1.4.4
[16] scales_1.3.0
[17] illuminaio_0.46.0
[18] limma_3.60.6
[19] gridExtra_2.3
[20] gplots_3.2.0
[21] fields_16.3
[22] viridisLite_0.4.2
[23] spam_2.11-1
[24] ff_4.5.2
[25] bit_4.5.0.1
[26] cluster_2.1.8
[27] MASS_7.3-64
[28] shinyMethyl_1.41.1
[29] methylclock_1.10.0
[30] quadprog_1.5-8
[31] devtools_2.4.5
[32] usethis_3.1.0
[33] methylclockData_1.12.0
[34] futile.logger_1.4.3
[35] sesame_1.22.2
[36] sesameData_1.22.0
[37] FlowSorted.BloodExtended.EPIC_1.1.1
[38] FlowSorted.Blood.EPIC_2.8.0
[39] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[40] ExperimentHub_2.12.0
[41] AnnotationHub_3.12.0
[42] BiocFileCache_2.12.0
[43] dbplyr_2.5.0
[44] data.table_1.16.4
[45] lubridate_1.9.4
[46] forcats_1.0.0
[47] stringr_1.5.1
[48] dplyr_1.1.4
[49] purrr_1.0.2
[50] readr_2.1.5
[51] tidyr_1.3.1
[52] tibble_3.2.1
[53] ggplot2_3.5.1
[54] tidyverse_2.0.0
[55] minfi_1.50.0
[56] bumphunter_1.46.0
[57] locfit_1.5-9.10
[58] iterators_1.0.14
[59] foreach_1.5.2
[60] Biostrings_2.72.1
[61] XVector_0.44.0
[62] SummarizedExperiment_1.34.0
[63] Biobase_2.64.0
[64] MatrixGenerics_1.16.0
[65] matrixStats_1.5.0
[66] GenomicRanges_1.56.2
[67] GenomeInfoDb_1.40.1
[68] IRanges_2.38.1
[69] S4Vectors_0.42.1
[70] BiocGenerics_0.50.0
[71] BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] progress_1.2.3 pacman_0.5.1
[3] ggpp_0.5.8-1 urlchecker_1.0.1
[5] RPMM_1.25 HDF5Array_1.32.1
[7] vctrs_0.6.5 digest_0.6.37
[9] png_0.1-8 plyranges_1.24.0
[11] BiocBaseUtils_1.6.0 PerformanceAnalytics_2.0.8
[13] reshape_0.8.9 httpuv_1.6.15
[15] withr_3.0.2 xfun_0.50
[17] ggpubr_0.6.0 ellipsis_0.3.2
[19] survival_3.8-3 doRNG_1.8.6.1
[21] memoise_2.0.1 MatrixModels_0.5-3
[23] profvis_0.4.0 zoo_1.8-12
[25] gtools_3.9.5 DNAcopy_1.78.0
[27] Formula_1.2-5 prettyunits_1.2.0
[29] KEGGREST_1.44.1 promises_1.3.2
[31] httr_1.4.7 rstatix_0.7.2
[33] restfulr_0.0.15 rhdf5filters_1.16.0
[35] ps_1.9.0 rhdf5_2.48.0
[37] rstudioapi_0.17.1 UCSC.utils_1.0.0
[39] miniUI_0.1.1.1 generics_0.1.3
[41] processx_3.8.5 curl_6.2.0
[43] zlibbioc_1.50.0 GenomeInfoDbData_1.2.12
[45] SparseArray_1.4.8 RBGL_1.80.0
[47] desc_1.4.3 xtable_1.8-4
[49] evaluate_1.0.3 S4Arrays_1.4.1
[51] preprocessCore_1.66.0 hms_1.1.3
[53] colorspace_2.1-1 filelock_1.0.3
[55] polynom_1.4-1 magrittr_2.0.3
[57] later_1.4.1 lattice_0.22-6
[59] genefilter_1.86.0 SparseM_1.84-2
[61] XML_3.99-0.18 xts_0.14.1
[63] pillar_1.10.1 nlme_3.1-166
[65] caTools_1.18.3 compiler_4.4.1
[67] stringi_1.8.4 GenomicAlignments_1.40.0
[69] crayon_1.5.3 abind_1.4-8
[71] BiocIO_1.14.0 codetools_0.2-20
[73] openssl_2.3.1 plotly_4.10.4
[75] multtest_2.60.0 mime_0.12
[77] splines_4.4.1 Rcpp_1.0.14
[79] quantreg_5.99.1 sparseMatrixStats_1.16.0
[81] BiocCheck_1.40.0 knitr_1.49
[83] blob_1.2.4 BiocVersion_3.19.1
[85] fs_1.6.5 DelayedMatrixStats_1.26.0
[87] pkgbuild_1.4.6 ggsignif_0.6.4
[89] Matrix_1.7-2 callr_3.7.6
[91] statmod_1.5.0 tzdb_0.4.0
[93] pkgconfig_2.0.3 tools_4.4.1
[95] cachem_1.1.0 RSQLite_2.3.9
[97] DBI_1.2.3 impute_1.78.0
[99] fastmap_1.2.0 rmarkdown_2.29
[101] Rsamtools_2.20.0 broom_1.0.7
[103] dotCall64_1.2 graph_1.82.0
[105] carData_3.0-5 scrime_1.3.5
[107] biocViews_1.72.0 yaml_2.3.10
[109] AnnotationForge_1.46.0 rtracklayer_1.64.0
[111] cli_3.6.3 siggenes_1.78.0
[113] txdbmaker_1.0.1 lifecycle_1.0.4
[115] askpass_1.2.1 ggpmisc_0.6.1
[117] lambda.r_1.2.4 sessioninfo_1.2.3
[119] backports_1.5.0 BiocParallel_1.38.0
[121] annotate_1.82.0 timechange_0.3.0
[123] gtable_0.3.6 rjson_0.2.23
[125] ggridges_0.5.6 jsonlite_1.8.9
[127] bitops_1.0-9 bit64_4.6.0-1
[129] base64_2.0.2 futile.options_1.0.1
[131] lazyeval_0.2.2 shiny_1.10.0
[133] dynamicTreeCut_1.63-1 htmltools_0.5.8.1
[135] rappdirs_0.3.3 formatR_1.14
[137] glue_1.8.0 httr2_1.1.0
[139] RCurl_1.98-1.16 InteractionSet_1.32.0
[141] mclust_6.1.1 R6_2.6.1
[143] rngtools_1.5.2 pkgload_1.4.0
[145] Rhdf5lib_1.26.0 AnnotationHubData_1.34.0
[147] beanplot_1.3.1 stringdist_0.9.15
[149] DelayedArray_0.30.1 tidyselect_1.2.1
[151] maps_3.4.2.1 xml2_1.3.6
[153] car_3.1-3 wheatmap_0.2.0
[155] munsell_0.5.1 KernSmooth_2.23-26
[157] nor1mix_1.3-3 htmlwidgets_1.6.4
[159] RColorBrewer_1.1-3 biomaRt_2.60.1
[161] rlang_1.1.5 remotes_2.5.0
[163] RUnit_0.4.33 ExperimentHubData_1.30.0
[165] OrganismDbi_1.46.0