lumi: Importing Methylation EPIC IDAT files
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Entering edit mode
Zach Roe ▴ 10
@zach-roe-11189
Last seen 13 months ago

I have EPIC IDAT files, when I load them using importMethyIDAT, 2 files are detected as HumanMethylation27 samples and 6 files as HumanMethylation450 samples.

What could be causing the incorrect detection of EPIC arrays? I have used this code prior to import 450K IDAT files.

> # Load Illumina EPIC sample map 
> idat_fileAnno <- read.csv(file.path(getwd(), 'idat_files_test', 'MiyanoShalabiEPIC_idat_fileAnno_test.csv'), header = T, stringsAsFactors = F)
> # Import Data 
> methylData.EPIC <- importMethyIDAT(sampleInfo=idat_fileAnno, dataPath='idat_files')

2 HumanMethylation27 samples found
6 HumanMethylation450 samples found
Error in methylumIDAT(barcodes = barcodes, pdat = pdat, parallel = parallel,  : 
Cannot process both platforms simultaneously; please run separately.


> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0
 [3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 lumi_2.32.0                                        
 [5] ChAMP_2.10.2                                        IlluminaHumanMethylationEPICmanifest_0.3.0         
 [7] Illumina450ProbeVariants.db_1.16.0                  DMRcate_1.16.0                                     
 [9] DMRcatedata_1.16.0                                  DSS_2.28.0                                         
[11] bsseq_1.16.1                                        FEM_3.8.0                                          
[13] graph_1.58.2                                        org.Hs.eg.db_3.6.0                                 
[15] impute_1.54.0                                       igraph_1.2.5                                       
[17] corrplot_0.84                                       marray_1.58.0                                      
[19] limma_3.36.5                                        Matrix_1.2-18                                      
[21] AnnotationDbi_1.42.1                                ChAMPdata_2.12.0                                   
[23] minfi_1.26.2                                        bumphunter_1.22.0                                  
[25] locfit_1.5-9.1                                      iterators_1.0.12                                   
[27] foreach_1.5.0                                       Biostrings_2.48.0                                  
[29] XVector_0.20.0                                      SummarizedExperiment_1.10.1                        
[31] DelayedArray_0.6.6                                  BiocParallel_1.14.2                                
[33] matrixStats_0.56.0                                  GenomicRanges_1.32.7                               
[35] GenomeInfoDb_1.16.0                                 IRanges_2.14.12                                    
[37] S4Vectors_0.18.3                                    reshape2_1.4.3                                     
[39] scales_1.1.0                                        Biobase_2.40.0                                     
[41] BiocGenerics_0.26.0                                

loaded via a namespace (and not attached):
  [1] R.utils_2.9.2                                      tidyselect_1.0.0                                  
  [3] RSQLite_2.2.0                                      htmlwidgets_1.5.1                                 
  [5] combinat_0.0-8                                     grid_3.5.0                                        
  [7] munsell_0.5.0                                      codetools_0.2-16                                  
  [9] preprocessCore_1.42.0                              nleqslv_3.3.2                                     
 [11] statmod_1.4.34                                     fastICA_1.2-2                                     
 [13] colorspace_1.4-1                                   BiocInstaller_1.30.0                              
 [15] knitr_1.28                                         rstudioapi_0.11                                   
 [17] JADE_2.0-2                                         isva_1.9                                          
 [19] GenomeInfoDbData_1.1.0                             bit64_0.9-7                                       
 [21] rhdf5_2.24.0                                       vctrs_0.2.4                                       
 [23] xfun_0.13                                          biovizBase_1.28.2                                 
 [25] doParallel_1.0.15                                  R6_2.4.1                                          
 [27] clue_0.3-57                                        illuminaio_0.22.0                                 
 [29] AnnotationFilter_1.4.0                             bitops_1.0-6                                      
 [31] reshape_0.8.8                                      assertthat_0.2.1                                  
 [33] promises_1.1.0                                     IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
 [35] nnet_7.3-13                                        gtable_0.3.0                                      
 [37] affy_1.58.0                                        methylumi_2.26.0                                  
 [39] sva_3.28.0                                         ensembldb_2.4.1                                   
 [41] rlang_0.4.5                                        genefilter_1.62.0                                 
 [43] rtracklayer_1.40.6                                 lazyeval_0.2.2                                    
 [45] acepack_1.4.1                                      GEOquery_2.48.0                                   
 [47] dichromat_2.0-0                                    checkmate_2.0.0                                   
 [49] BiocManager_1.30.10                                yaml_2.2.1                                        
 [51] GenomicFeatures_1.32.3                             backports_1.1.5                                   
 [53] httpuv_1.5.2                                       qvalue_2.12.0                                     
 [55] Hmisc_4.3-1                                        tools_3.5.0                                       
 [57] nor1mix_1.3-0                                      ggplot2_3.3.0                                     
 [59] affyio_1.50.0                                      RColorBrewer_1.1-2                                
 [61] DNAcopy_1.54.0                                     siggenes_1.54.0                                   
 [63] Rcpp_1.0.4                                         plyr_1.8.6                                        
 [65] ROC_1.56.0                                         base64enc_0.1-3                                   
 [67] progress_1.2.2                                     zlibbioc_1.26.0                                   
 [69] purrr_0.3.3                                        RCurl_1.98-1.1                                    
 [71] BiasedUrn_1.07                                     prettyunits_1.1.1                                 
 [73] rpart_4.1-15                                       openssl_1.4.1                                     
 [75] viridis_0.5.1                                      cluster_2.1.0                                     
 [77] magrittr_1.5                                       data.table_1.12.8                                 
 [79] goseq_1.32.0                                       wateRmelon_1.24.0                                 
 [81] ProtGenerics_1.12.0                                missMethyl_1.14.0                                 
 [83] RPMM_1.25                                          evaluate_0.14                                     
 [85] mime_0.9                                           hms_0.5.3                                         
 [87] xtable_1.8-4                                       globaltest_5.34.1                                 
 [89] XML_3.99-0.3                                       mclust_5.4.5                                      
 [91] gridExtra_2.3                                      compiler_3.5.0                                    
 [93] biomaRt_2.36.1                                     tibble_2.1.3                                      
 [95] KernSmooth_2.23-16                                 crayon_1.3.4                                      
 [97] R.oo_1.23.0                                        htmltools_0.4.0                                   
 [99] later_1.0.0                                        mgcv_1.8-31                                       
[101] Formula_1.2-3                                      tidyr_1.0.2                                       
[103] DBI_1.1.0                                          geneLenDataBase_1.16.0                            
[105] MASS_7.3-51.5                                      readr_1.3.1                                       
[107] permute_0.9-5                                      cli_2.0.2                                         
[109] quadprog_1.5-8                                     R.methodsS3_1.8.0                                 
[111] Gviz_1.24.0                                        pkgconfig_2.0.3                                   
[113] GenomicAlignments_1.16.0                           IlluminaHumanMethylation450kmanifest_0.4.0        
[115] foreign_0.8-76                                     plotly_4.9.2.1                                    
[117] xml2_1.2.5                                         annotate_1.58.0                                   
[119] rngtools_1.5                                       multtest_2.36.0                                   
[121] beanplot_1.2                                       ruv_0.9.7.1                                       
[123] doRNG_1.8.2                                        stringr_1.4.0                                     
[125] VariantAnnotation_1.26.1                           digest_0.6.25                                     
[127] rmarkdown_2.1                                      base64_2.0                                        
[129] htmlTable_1.13.3                                   dendextend_1.13.4                                 
[131] DelayedMatrixStats_1.2.0                           curl_4.3                                          
[133] shiny_1.4.0.2                                      Rsamtools_1.32.3                                  
[135] gtools_3.8.1                                       jsonlite_1.6.1                                    
[137] lifecycle_0.2.0                                    nlme_3.1-145                                      
[139] Rhdf5lib_1.2.1                                     viridisLite_0.3.0                                 
[141] askpass_1.1                                        BSgenome_1.48.0                                   
[143] fansi_0.4.1                                        pillar_1.4.3                                      
[145] lattice_0.20-40                                    fastmap_1.0.1                                     
[147] httr_1.4.1                                         survival_3.1-11                                   
[149] GO.db_3.6.0                                        glue_1.3.2                                        
[151] shinythemes_1.1.2                                  bit_1.1-15.2                                      
[153] stringi_1.4.6                                      HDF5Array_1.8.1                                   
[155] blob_1.2.1                                         latticeExtra_0.6-28                               
[157] memoise_1.1.0                                      dplyr_0.8.5
lumi EPIC Methylation • 145 views
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2
Entering edit mode
lhuang7 ▴ 50
@lhuang7-7824
Last seen 13 months ago
United States

Function methylumIDAT() is from package methylumi. It seems the EPIC data is not supported if you look at the source code for that function:

hm27 = hm450 = 0
hm27 = sum(!grepl("_R0[123456]C0[12]", barcodes))
message(paste(hm27, "HumanMethylation27 samples found"))
hm450 = sum(grepl("_R0[123456]C0[12]", barcodes))
message(paste(hm450, "HumanMethylation450 samples found"))
if (hm27 > 0 && hm450 > 0) {
    stop("Cannot process both platforms simultaneously; please run separately.")
}

You could use functions from other BioC packages such as wateRmelon to read EPIC data.

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