Hello, i am working on DNA methylation data analysis in R on a server and performing QC but when i run the preprocessnoob function im getting this error Error in matrixStats::colMeans2(x, rows = rows, cols = cols, na.rm = na.rm, : Argument 'useNames' must be either TRUE or FALSE . How can i avoid it?

# This script will perform QC for DNA methylation data

# Upload necessary packages/libraries
packages <- c("minfi", "RColorBrewer", "illuminaio",
              "IlluminaHumanMethylationEPICmanifest",
              "IlluminaHumanMethylationEPICanno.ilm10b4.hg19", "ggplot2", "readr")

for (pkg in packages) {
  if (!require(pkg, character.only = TRUE)) {
    if (pkg %in% c("minfi", "illuminaio", "IlluminaHumanMethylationEPICmanifest", "IlluminaHumanMethylationEPICanno.ilm10b4.hg19")) {
      BiocManager::install(pkg, force = TRUE)
    } else {
      install.packages(pkg)
    }
  }
  library(pkg, character.only = TRUE)
}


# Seeting directory
setwd("~path1/idats")
data_directory <- "~path2/EPIC"
base_directory <- "~/path1/idats/"

# uploading and organizing the samplesheet that contains the methyation infos
samplesheet <- read.metharray.sheet(data_directory, pattern = "samplesheet.csv")

# Read IDAT files using minfi 
rgSet <- read.metharray.exp(targets = samplesheet)
pd <- pData(rgSet) # extract the data in rgSet as a Data frame, not necessary 
manifest <- getManifest(rgSet)
manifest
head(getProbeInfo(manifest))

# give tyhe samples descriptive names

# Pre-Normalization QC (Optional Visual Check)
densityPlot(rgSet, main = "Raw Intensities")
controlStripPlot(rgSet) # Control probes visualization: This plot is part of the quality control to check bisulfite conversion efficiency. 
qc_report_path <- file.path(data_directory, "qc_report_raw.pdf") 
qcReport(rgSet, pdf = qc_report_path) 
qcReport(rgSet, pdf = "qc_report_raw.pdf")


# QC after normalization
# Normalization using preprocessNoob so we can have 'MethylSet' Object for QC
mset_noob <- preprocessNoob(rgSet)

qc <- getQC(mset_noob)
plotQC(qc)
densityPlot(mset_noob, main = "Normalized Beta Values")



    sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so

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

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

other attached packages:
 [1] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 readr_2.1.5                                        
 [3] illuminaio_0.40.0                                   ggplot2_3.5.1                                      
 [5] RColorBrewer_1.1-3                                  IlluminaHumanMethylationEPICmanifest_0.3.0         
 [7] minfi_1.44.0                                        bumphunter_1.40.0                                  
 [9] locfit_1.5-9.11                                     iterators_1.0.14                                   
[11] foreach_1.5.2                                       Biostrings_2.66.0                                  
[13] XVector_0.38.0                                      SummarizedExperiment_1.28.0                        
[15] Biobase_2.58.0                                      MatrixGenerics_1.10.0                              
[17] matrixStats_1.5.0                                   GenomicRanges_1.50.2                               
[19] GenomeInfoDb_1.34.9                                 IRanges_2.32.0                                     
[21] S4Vectors_0.36.2                                    BiocGenerics_0.44.0                                
[23] BiocManager_1.30.25                                

loaded via a namespace (and not attached):
  [1] colorspace_2.1-1          rjson_0.2.23              siggenes_1.72.0           mclust_6.1.1             
  [5] base64_2.0.2              rstudioapi_0.17.1         bit64_4.6.0-1             AnnotationDbi_1.60.2     
  [9] xml2_1.3.6                codetools_0.2-19          splines_4.2.3             sparseMatrixStats_1.10.0 
 [13] cachem_1.1.0              scrime_1.3.5              knitr_1.49                Rsamtools_2.14.0         
 [17] gt_0.11.1                 annotate_1.76.0           dbplyr_2.5.0              png_0.1-8                
 [21] HDF5Array_1.26.0          compiler_4.2.3            httr_1.4.7                Matrix_1.5-3             
 [25] fastmap_1.2.0             limma_3.54.2              cli_3.6.4                 htmltools_0.5.8.1        
 [29] prettyunits_1.2.0         tools_4.2.3               gtable_0.3.6              glue_1.8.0               
 [33] GenomeInfoDbData_1.2.9    dplyr_1.1.4               rappdirs_0.3.3            doRNG_1.8.6.1            
 [37] Rcpp_1.0.14               cellranger_1.1.0          vctrs_0.6.5               rhdf5filters_1.10.1      
 [41] multtest_2.54.0           preprocessCore_1.60.2     nlme_3.1-162              rtracklayer_1.58.0       
 [45] DelayedMatrixStats_1.20.0 xfun_0.51                 stringr_1.5.1             lifecycle_1.0.4          
 [49] restfulr_0.0.15           rngtools_1.5.2            XML_3.99-0.18             beanplot_1.3.1           
 [53] zlibbioc_1.44.0           MASS_7.3-58.2             scales_1.3.0              ragg_1.3.3               
 [57] hms_1.1.3                 rhdf5_2.42.1              GEOquery_2.66.0           yaml_2.3.10              
 [61] curl_6.2.1                memoise_2.0.1             biomaRt_2.54.1            reshape_0.8.9            
 [65] stringi_1.8.4             RSQLite_2.3.9             genefilter_1.80.3         BiocIO_1.8.0             
 [69] GenomicFeatures_1.50.4    filelock_1.0.3            BiocParallel_1.32.6       systemfonts_1.2.1        
 [73] rlang_1.1.5               pkgconfig_2.0.3           bitops_1.0-9              nor1mix_1.3-3            
 [77] evaluate_1.0.3            lattice_0.20-45           purrr_1.0.4               Rhdf5lib_1.20.0          
 [81] GenomicAlignments_1.34.1  bit_4.5.0.1               tidyselect_1.2.1          plyr_1.8.9               
 [85] magrittr_2.0.3            R6_2.6.1                  generics_0.1.3            DelayedArray_0.24.0      
 [89] DBI_1.2.3                 withr_3.0.2               pillar_1.10.1             survival_3.5-3           
 [93] KEGGREST_1.38.0           RCurl_1.98-1.16           tibble_3.2.1              crayon_1.5.3             
 [97] BiocFileCache_2.6.1       rmarkdown_2.29            tzdb_0.4.0                progress_1.2.3           
[101] readxl_1.4.3              grid_4.2.3                data.table_1.16.4         blob_1.2.4               
[105] digest_0.6.37             xtable_1.8-4              tidyr_1.3.1               textshaping_1.0.0        
[109] munsell_0.5.1             openssl_2.3.2             sessioninfo_1.2.3         askpass_1.2.1            
[113] quadprog_1.5-8 

Your code doesn't show the error?

Anyway, the default for colMeans2 is useNames = TRUE, and the call to colMeans2 in preprocessNoob doesn't have an ellipsis argument, so I don't see how the argument is getting set to anything but the default. Given that, you will probably have to run under the debugger and figure it out for yourself.

debug(minfi:::dyeCorrection)
mset_noob <- preprocessNoob(rgSet)

And then step through the debugger until you get to this part:

 # Dye bias normalization with the corrected Illumina control probes
    Green.avg <- colMeans2(x = internal.controls[["Green"]], rows = CG.controls)
    Red.avg <- colMeans2(x = internal.controls[["Red"]], rows = AT.controls)

and try to figure out how the useNames argument is being set.