champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
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@arisarkar88-11464
Last seen 1 day ago
Los Angeles

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!

methylationArrayAnalysis EPICarray ChAMP Champ.SVD • 49 views
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[SVD analysis will be proceed with 0 probes and 32 samples.]

0 probes so you need to check what is your myNorm

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Works now. Thanks!

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