I've been trying to analyze data collected using the EPIC V2 array and have been running into issues using the preprocessIllumina function. I should be using the correct version of the EPICv2 manifest (see the first line of the script and the sessionInfo for the loaded R libraries).

> meth@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38")

> MSet.norm<-preprocessIllumina(meth, bg.correct = TRUE, normalize = "no")
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'X' in selecting a method for function 'apply': object 'NegControls' not found

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 9.2 (Blue Onyx)

Matrix products: default
BLAS/LAPACK: /data/apps/software/spack/linux-rocky9-x86_64_v3/gcc-11.3.1/openblas-0.3.27-fvnsluafkwg3hhnlpvj34jtx657mywxl/lib/libopenblas-r0.3.27.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] IlluminaHumanMethylationEPICv2manifest_1.0.0      
 [2] IlluminaHumanMethylationEPICv2anno.20a1.hg38_1.0.0
 [3] ENmix_1.40.2                                      
 [4] doParallel_1.0.17                                 
 [5] stringr_1.5.1                                     
 [6] minfi_1.50.0                                      
 [7] bumphunter_1.46.0                                 
 [8] locfit_1.5-9.10                                   
 [9] iterators_1.0.14                                  
[10] foreach_1.5.2                                     
[11] Biostrings_2.72.1                                 
[12] XVector_0.44.0                                    
[13] SummarizedExperiment_1.34.0                       
[14] Biobase_2.64.0                                    
[15] MatrixGenerics_1.16.0                             
[16] matrixStats_1.4.1                                 
[17] GenomicRanges_1.56.2                              
[18] GenomeInfoDb_1.40.1                               
[19] IRanges_2.38.1                                    
[20] S4Vectors_0.42.1                                  
[21] BiocGenerics_0.50.0                               
[22] ggplot2_3.5.1                                     
[23] dplyr_1.1.4                                       

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3        jsonlite_1.8.9           
  [3] magrittr_2.0.3            GenomicFeatures_1.56.0   
  [5] BiocIO_1.14.0             zlibbioc_1.50.0          
  [7] vctrs_0.6.5               multtest_2.60.0          
  [9] memoise_2.0.1             Rsamtools_2.20.0         
 [11] DelayedMatrixStats_1.26.0 RCurl_1.98-1.16          
 [13] askpass_1.2.1             S4Arrays_1.4.1           
 [15] AnnotationHub_3.12.0      dynamicTreeCut_1.63-1    
 [17] curl_5.2.3                Rhdf5lib_1.26.0          
 [19] RPMM_1.25                 SparseArray_1.4.8        
 [21] rhdf5_2.48.0              KernSmooth_2.23-24       
 [23] nor1mix_1.3-3             plyr_1.8.9               
 [25] impute_1.78.0             cachem_1.1.0             
 [27] GenomicAlignments_1.40.0  lifecycle_1.0.4          
 [29] pkgconfig_2.0.3           Matrix_1.7-0             
 [31] R6_2.5.1                  fastmap_1.2.0            
 [33] GenomeInfoDbData_1.2.12   digest_0.6.37            
 [35] colorspace_2.1-1          siggenes_1.78.0          
 [37] reshape_0.8.9             AnnotationDbi_1.66.0     
 [39] irlba_2.3.5.1             ExperimentHub_2.12.0     
 [41] geneplotter_1.82.0        RSQLite_2.3.7            
 [43] base64_2.0.2              filelock_1.0.3           
 [45] fansi_1.0.6               httr_1.4.7               
 [47] abind_1.4-8               compiler_4.4.1           
 [49] beanplot_1.3.1            rngtools_1.5.2           
 [51] bit64_4.5.2               withr_3.0.1              
 [53] BiocParallel_1.38.0       DBI_1.2.3                
 [55] gplots_3.2.0              HDF5Array_1.32.1         
 [57] MASS_7.3-61               openssl_2.2.2            
 [59] rappdirs_0.3.3            DelayedArray_0.30.1      
 [61] rjson_0.2.23              caTools_1.18.3           
 [63] gtools_3.9.5              tools_4.4.1              
 [65] glue_1.8.0                quadprog_1.5-8           
 [67] restfulr_0.0.15           nlme_3.1-166             
 [69] rhdf5filters_1.16.0       grid_4.4.1               
 [71] cluster_2.1.6             generics_0.1.3           
 [73] gtable_0.3.5              tzdb_0.4.0               
 [75] preprocessCore_1.66.0     tidyr_1.3.1              
 [77] data.table_1.16.2         hms_1.1.3                
 [79] xml2_1.3.6                utf8_1.2.4               
 [81] BiocVersion_3.19.1        pillar_1.9.0             
 [83] limma_3.60.6              genefilter_1.86.0        
 [85] splines_4.4.1             BiocFileCache_2.12.0     
 [87] lattice_0.22-6            survival_3.7-0           
 [89] rtracklayer_1.64.0        bit_4.5.0                
 [91] GEOquery_2.72.0           annotate_1.82.0          
 [93] tidyselect_1.2.1          scrime_1.3.5             
 [95] statmod_1.5.0             stringi_1.8.4            
 [97] UCSC.utils_1.0.0          yaml_2.3.10              
 [99] codetools_0.2-20          tibble_3.2.1             
[101] BiocManager_1.30.25       cli_3.6.3                
[103] xtable_1.8-4              munsell_0.5.1            
[105] Rcpp_1.0.13               dbplyr_2.5.0             
[107] png_0.1-8                 XML_3.99-0.14            
[109] readr_2.1.5               blob_1.2.4               
[111] mclust_6.1.1              doRNG_1.8.6              
[113] sparseMatrixStats_1.16.0  bitops_1.0-9             
[115] scales_1.3.0              illuminaio_0.46.0        
[117] purrr_1.0.2               crayon_1.5.3             
[119] rlang_1.1.4               KEGGREST_1.44.1

I believe the error might be attributable to the fact that, in the code for the bgcorrect.illumina function (which is called by preprocessIllumina), the conditional statements don't include the V2 array (relevant excerpt):

    if (.is450k(rgSet) || .isEPIC(rgSet) || .isAllergy(rgSet)) {
        NegControls <- getControlAddress(rgSet, controlType = "NEGATIVE")
    }
    if (.is27k(rgSet)) {
        NegControls <- getControlAddress(rgSet, controlType = "Negative")
    }

Does anyone know how to resolve this issue? Is it as simple as adding:

.isEPICv2 <- function(object) {
    annotation(object)["array"] == "IlluminaHumanMethylationEPICv2"
}

to the utils.R file and updating the preprocessIllumina function to state:

    if (.is450k(rgSet) || .isEPIC(rgSet) || .isAllergy(rgSet) || .isEPICv2(rgSet)) {
        NegControls <- getControlAddress(rgSet, controlType = "NEGATIVE")
    }
    if (.is27k(rgSet)) {
        NegControls <- getControlAddress(rgSet, controlType = "Negative")
    }