Entering edit mode
Hi, I am trying to analyze EPIC array methylation using the package Champ. However after normalization when I try running SVD I get the following error:
> champ.SVD()
[SVD analysis will be proceed with 0 probes and 32 samples.]
[ champ.SVD() will only check the dimensions between data and pd, instead if checking if Sample_Names are correctly matched (because some user may have no Sample_Names in their pd file),thus please make sure your pd file is in accord with your data sets (beta) and (rgSet).]
<< Following Factors in your pd(sample_sheet.csv) will be analysised: >>
<ID>(character):treatment1,treatment2,control
<PlateIndex>(character):Plate 01, Plate 02
<WellAddressIndex>(character):B01, C01, D01, G01, B02, E02, H02, C03, E03, F03, G03, H03, A04, B04, C04, D04, F04, D05, F05, F02, A07, G04, F07, H04, A05, B05, D06, E06, F06, A02, H06, C08
<Batch>(integer):1, 2
<Age>(numeric):-0.49, -0.47, -0.46, -0.45, -0.44, -0.42, -0.40, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85
<Type>(character):treatment1,treatment2,control
<Sample_Group>(character):treatment1,treatment2,control
[champ.SVD have automatically select ALL factors contain at least two different values from your pd(sample_sheet.csv), if you don't want to analysis some of them, please remove them manually from your pd variable then retry champ.SVD().]
<< Following Factors in your pd(sample_sheet.csv) will not be analysis: >>
<Basename>
<Sample_Name>
<filenames>
[Factors are ignored because they only indicate Name or Project, or they contain ONLY ONE value across all Samples.]
<< PhenoTypes.lv generated successfully. >>
Error in while (step == 0) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In if (class(beta) == "data.frame") { :
the condition has length > 1 and only the first element will be used
> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[2] shiny_1.6.0
[3] doParallel_1.0.16
[4] ChAMP_2.20.1
[5] RPMM_1.25
[6] cluster_2.1.1
[7] DT_0.17
[8] IlluminaHumanMethylationEPICmanifest_0.3.0
[9] Illumina450ProbeVariants.db_1.26.0
[10] DMRcate_2.4.1
[11] ChAMPdata_2.22.0
[12] minfi_1.36.0
[13] bumphunter_1.32.0
[14] locfit_1.5-9.4
[15] iterators_1.0.13
[16] foreach_1.5.1
[17] Biostrings_2.58.0
[18] XVector_0.30.0
[19] SummarizedExperiment_1.20.0
[20] Biobase_2.50.0
[21] MatrixGenerics_1.2.1
[22] matrixStats_0.58.0
[23] GenomicRanges_1.42.0
[24] GenomeInfoDb_1.26.4
[25] IRanges_2.24.1
[26] S4Vectors_0.28.1
[27] BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3
[2] rtracklayer_1.50.0
[3] R.methodsS3_1.8.1
[4] wateRmelon_1.34.0
[5] tidyr_1.1.3
[6] ggplot2_3.3.3
[7] bit64_4.0.5
[8] knitr_1.31
[9] DelayedArray_0.16.3
[10] R.utils_2.10.1
[11] data.table_1.14.0
[12] rpart_4.1-15
[13] RCurl_1.98-1.3
[14] GEOquery_2.58.0
[15] AnnotationFilter_1.14.0
[16] generics_0.1.0
[17] GenomicFeatures_1.42.3
[18] preprocessCore_1.52.1
[19] RSQLite_2.2.5
[20] combinat_0.0-8
[21] bit_4.0.4
[22] xml2_1.3.2
[23] httpuv_1.5.5
[24] assertthat_0.2.1
[25] IlluminaHumanMethylation450kmanifest_0.4.0
[26] viridis_0.5.1
[27] isva_1.9
[28] xfun_0.22
[29] jquerylib_0.1.3
[30] hms_1.0.0
[31] evaluate_0.14
[32] missMethyl_1.24.0
[33] DNAcopy_1.64.0
[34] promises_1.2.0.1
[35] fansi_0.4.2
[36] scrime_1.3.5
[37] progress_1.2.2
[38] dendextend_1.14.0
[39] dbplyr_2.1.0
[40] DBI_1.1.1
[41] htmlwidgets_1.5.3
[42] reshape_0.8.8
[43] purrr_0.3.4
[44] ROC_1.66.0
[45] ellipsis_0.3.1
[46] crosstalk_1.1.1
[47] dplyr_1.0.5
[48] backports_1.2.1
[49] permute_0.9-5
[50] annotate_1.68.0
[51] biomaRt_2.46.3
[52] sparseMatrixStats_1.2.1
[53] vctrs_0.3.7
[54] ensembldb_2.14.0
[55] cachem_1.0.4
[56] globaltest_5.44.0
[57] Gviz_1.34.1
[58] BSgenome_1.58.0
[59] checkmate_2.0.0
[60] GenomicAlignments_1.26.0
[61] prettyunits_1.1.1
[62] mclust_5.4.7
[63] ExperimentHub_1.16.0
[64] lazyeval_0.2.2
[65] crayon_1.4.1
[66] genefilter_1.72.1
[67] edgeR_3.32.1
[68] pkgconfig_2.0.3
[69] nlme_3.1-152
[70] ProtGenerics_1.22.0
[71] nnet_7.3-15
[72] rlang_0.4.10
[73] lifecycle_1.0.0
[74] nleqslv_3.3.2
[75] affyio_1.60.0
[76] BiocFileCache_1.14.0
[77] AnnotationHub_2.22.0
[78] dichromat_2.0-0
[79] rngtools_1.5
[80] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[81] base64_2.0
[82] Matrix_1.3-2
[83] Rhdf5lib_1.12.1
[84] base64enc_0.1-3
[85] geneLenDataBase_1.26.0
[86] png_0.1-7
[87] viridisLite_0.3.0
[88] bitops_1.0-6
[89] R.oo_1.24.0
[90] KernSmooth_2.23-18
[91] rhdf5filters_1.2.0
[92] blob_1.2.1
[93] DelayedMatrixStats_1.12.3
[94] doRNG_1.8.2
[95] stringr_1.4.0
[96] qvalue_2.22.0
[97] nor1mix_1.3-0
[98] readr_1.4.0
[99] jpeg_0.1-8.1
[100] scales_1.1.1
[101] memoise_2.0.0
[102] magrittr_2.0.1
[103] plyr_1.8.6
[104] zlibbioc_1.36.0
[105] compiler_4.0.3
[106] RColorBrewer_1.1-2
[107] illuminaio_0.32.0
[108] clue_0.3-58
[109] Rsamtools_2.6.0
[110] DSS_2.38.0
[111] affy_1.68.0
[112] JADE_2.0-3
[113] htmlTable_2.1.0
[114] Formula_1.2-4
[115] MASS_7.3-53.1
[116] mgcv_1.8-34
[117] tidyselect_1.1.0
[118] stringi_1.5.3
[119] yaml_2.2.1
[120] askpass_1.1
[121] latticeExtra_0.6-29
[122] grid_4.0.3
[123] sass_0.3.1
[124] VariantAnnotation_1.36.0
[125] tools_4.0.3
[126] rstudioapi_0.13
[127] foreign_0.8-81
[128] bsseq_1.26.0
[129] gridExtra_2.3
[130] farver_2.1.0
[131] digest_0.6.27
[132] BiocManager_1.30.12
[133] quadprog_1.5-8
[134] Rcpp_1.0.6
[135] siggenes_1.64.0
[136] BiocVersion_3.12.0
[137] later_1.1.0.1
[138] org.Hs.eg.db_3.12.0
[139] httr_1.4.2
[140] AnnotationDbi_1.52.0
[141] biovizBase_1.38.0
[142] lumi_2.42.0
[143] colorspace_2.0-0
[144] XML_3.99-0.6
[145] splines_4.0.3
[146] statmod_1.4.35
[147] kpmt_0.1.0
[148] multtest_2.46.0
[149] shinythemes_1.2.0
[150] plotly_4.9.3
[151] xtable_1.8-4
[152] jsonlite_1.7.2
[153] marray_1.68.0
[154] R6_2.5.0
[155] Hmisc_4.5-0
[156] pillar_1.5.1
[157] htmltools_0.5.1.1
[158] mime_0.10
[159] glue_1.4.2
[160] fastmap_1.1.0
[161] BiocParallel_1.24.1
[162] interactiveDisplayBase_1.28.0
[163] beanplot_1.2
[164] codetools_0.2-18
[165] utf8_1.2.1
[166] bslib_0.2.4
[167] lattice_0.20-41
[168] tibble_3.1.0
[169] sva_3.38.0
[170] BiasedUrn_1.07
[171] curl_4.3
[172] gtools_3.8.2
[173] GO.db_3.12.1
[174] openssl_1.4.3
[175] survival_3.2-10
[176] limma_3.46.0
[177] rmarkdown_2.7
[178] methylumi_2.36.0
[179] fastICA_1.2-2
[180] munsell_0.5.0
[181] rhdf5_2.34.0
[182] GenomeInfoDbData_1.2.4
[183] goseq_1.42.0
[184] HDF5Array_1.18.1
[185] impute_1.64.0
[186] reshape2_1.4.4
[187] gtable_0.3.0
Any help or suggestion is highly appreciated. Thanks!
0 probes so you need to check what is your myNorm
Works now. Thanks!