Entering edit mode
Hi, I am a beginner in epigenetic analyses. I am using the Meffil package and pipeline in preprocessing my DNA methylation data. I performed QC, extracted SNPs, removed 4 outlier samples, and performed quantile normalization. For running the function below, this error occurs. The function does work for a subselection of the first 5 samples which I find confusing. Does anyone recognize this error, knows why it came to disturb, and even better - knows how to fix it? Thanks a million!
Anne
PS I am using an older version of R/RStudio because Meffil has not been updated yet.
> norm.objects <- meffil.normalize.quantiles(qc.objects, number.pcs=pc)
> norm.beta <- meffil.normalize.samples(norm.objects, cpglist.remove = qc.summary$bad.cpgs$name)
Error in rg.to.mu(rg, probes) :
all(c(probes.M.R$address, probes.U.R$address) %in% rownames(rg$R)) is not TRUE
> sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Netherlands.utf8 LC_CTYPE=Dutch_Netherlands.utf8
[3] LC_MONETARY=Dutch_Netherlands.utf8 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.utf8
time zone: Europe/Amsterdam
tzcode source: internal
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] meffil_1.3.6 preprocessCore_1.62.1 SmartSVA_0.1.3 RSpectra_0.16-2
[5] isva_1.9 JADE_2.0-4 qvalue_2.32.0 gdsfmt_1.36.1
[9] statmod_1.5.0 quadprog_1.5-8 DNAcopy_1.74.1 fastICA_1.2-7
[13] lme4_1.1-36 Matrix_1.6-3 multcomp_1.4-26 TH.data_1.1-3
[17] survival_3.5-8 mvtnorm_1.3-3 matrixStats_1.5.0 markdown_1.13
[21] gridExtra_2.3 Cairo_1.6-2 knitr_1.49 reshape2_1.4.4
[25] plyr_1.8.9 sva_3.48.0 BiocParallel_1.34.2 genefilter_1.82.1
[29] mgcv_1.9-1 nlme_3.1-164 limma_3.56.2 sandwich_3.1-1
[33] lmtest_0.9-40 zoo_1.8-12 MASS_7.3-60.0.1 illuminaio_0.42.0
[37] tidyr_1.3.1 dplyr_1.1.4 ggplot2_3.5.1 devtools_2.4.5
[41] usethis_3.1.0 BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] Rdpack_2.6.2 DBI_1.2.3 bitops_1.0-9
[4] remotes_2.5.0 rlang_1.1.2 magrittr_2.0.3
[7] clue_0.3-66 compiler_4.3.3 RSQLite_2.3.9
[10] png_0.1-8 vctrs_0.6.4 stringr_1.5.1
[13] profvis_0.4.0 pkgconfig_2.0.3 crayon_1.5.3
[16] fastmap_1.2.0 XVector_0.40.0 ellipsis_0.3.2
[19] promises_1.3.2 sessioninfo_1.2.2 nloptr_2.1.1
[22] purrr_1.0.2 bit_4.5.0.1 xfun_0.50
[25] zlibbioc_1.46.0 cachem_1.1.0 GenomeInfoDb_1.36.4
[28] blob_1.2.4 later_1.4.1 cluster_2.1.6
[31] R6_2.5.1 stringi_1.8.4 boot_1.3-29
[34] pkgload_1.4.0 Rcpp_1.0.14 IRanges_2.34.1
[37] httpuv_1.6.15 splines_4.3.3 tidyselect_1.2.1
[40] rstudioapi_0.17.1 codetools_0.2-19 miniUI_0.1.1.1
[43] pkgbuild_1.4.6 lattice_0.22-5 tibble_3.2.1
[46] Biobase_2.60.0 shiny_1.10.0 withr_3.0.2
[49] KEGGREST_1.40.1 askpass_1.2.1 evaluate_1.0.3
[52] urlchecker_1.0.1 Biostrings_2.68.1 pillar_1.10.1
[55] MatrixGenerics_1.14.0 stats4_4.3.3 reformulas_0.4.0
[58] generics_0.1.3 RCurl_1.98-1.16 S4Vectors_0.38.2
[61] munsell_0.5.1 scales_1.3.0 minqa_1.2.8
[64] xtable_1.8-4 glue_1.6.2 tools_4.3.3
[67] annotate_1.78.0 locfit_1.5-9.10 fs_1.6.5
[70] XML_3.99-0.18 grid_4.3.3 rbibutils_2.3
[73] AnnotationDbi_1.62.2 edgeR_3.42.4 colorspace_2.1-1
[76] base64_2.0.2 GenomeInfoDbData_1.2.10 cli_3.6.1
[79] gtable_0.3.6 digest_0.6.37 BiocGenerics_0.46.0
[82] htmlwidgets_1.6.4 memoise_2.0.1 htmltools_0.5.8.1
[85] lifecycle_1.0.4 httr_1.4.7 mime_0.12
[88] openssl_2.3.1 bit64_4.6.0-1
