MissMethyl failed to use gometh function for EPICv2
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@c0218f44
Last seen 1 day ago
Hong Kong

I try to use missMethyl to do gometh function for EPICv2 array, but it fails to do so. The latest released version should be formally support EPICv2. I have downloaded the latest version of missmethyl When I type ?gometh, it shows only array.type = c("450K", "EPIC"), no option for EPICv2. Despite the reference manual clear states we can select EPICv2 How can I solve the problem? Thanks.

sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22000)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Asia/Hong_Kong
tzcode source: internal

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

other attached packages:
 [1] missMethyl_1.38.0                                   IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 
 [4] minfi_1.50.0                                        bumphunter_1.46.0                                   locfit_1.5-9.10                                    
 [7] iterators_1.0.14                                    foreach_1.5.2                                       Biostrings_2.72.1                                  
[10] XVector_0.44.0                                      SummarizedExperiment_1.34.0                         Biobase_2.64.0                                     
[13] MatrixGenerics_1.16.0                               matrixStats_1.3.0                                   GenomicRanges_1.56.1                               
[16] GenomeInfoDb_1.40.1                                 IRanges_2.38.1                                      S4Vectors_0.42.1                                   
[19] BiocGenerics_0.50.0                                 BiocManager_1.30.23                                

loaded via a namespace (and not attached):
  [1] splines_4.4.1             BiocIO_1.14.0             bitops_1.0-8              filelock_1.0.3            tibble_3.2.1              R.oo_1.26.0              
  [7] preprocessCore_1.66.0     XML_3.99-0.17             rpart_4.1.23              lifecycle_1.0.4           httr2_1.0.2               edgeR_4.2.1              
 [13] base64_2.0.1              lattice_0.22-6            ensembldb_2.28.0          MASS_7.3-60.2             scrime_1.3.5              backports_1.5.0          
 [19] magrittr_2.0.3            limma_3.60.4              Hmisc_5.1-3               rmarkdown_2.27            yaml_2.3.10               doRNG_1.8.6              
 [25] askpass_1.2.0             Gviz_1.48.0               DBI_1.2.3                 RColorBrewer_1.1-3        DMRcate_3.0.5             abind_1.4-5              
 [31] zlibbioc_1.50.0           quadprog_1.5-8            purrr_1.0.2               R.utils_2.12.3            AnnotationFilter_1.28.0   biovizBase_1.52.0        
 [37] RCurl_1.98-1.16           nnet_7.3-19               VariantAnnotation_1.50.0  rappdirs_0.3.3            GenomeInfoDbData_1.2.12   genefilter_1.86.0        
 [43] pheatmap_1.0.12           annotate_1.82.0           permute_0.9-7             DelayedMatrixStats_1.26.0 codetools_0.2-20          DelayedArray_0.30.1      
 [49] DNAcopy_1.78.0            xml2_1.3.6                tidyselect_1.2.1          UCSC.utils_1.0.0          beanplot_1.3.1            BiocFileCache_2.12.0     
 [55] base64enc_0.1-3           illuminaio_0.46.0         GenomicAlignments_1.40.0  jsonlite_1.8.8            multtest_2.60.0           Formula_1.2-5            
 [61] survival_3.6-4            tools_4.4.1               progress_1.2.3            Rcpp_1.0.13               glue_1.7.0                gridExtra_2.3            
 [67] SparseArray_1.4.8         xfun_0.46                 dplyr_1.1.4               HDF5Array_1.32.0          fastmap_1.2.0             latticeExtra_0.6-30      
 [73] rhdf5filters_1.16.0       fansi_1.0.6               openssl_2.2.0             digest_0.6.36             R6_2.5.1                  colorspace_2.1-1         
 [79] gtools_3.9.5              jpeg_0.1-10               dichromat_2.0-0.1         biomaRt_2.60.1            RSQLite_2.3.7             R.methodsS3_1.8.2        
 [85] tidyr_1.3.1               utf8_1.2.4                generics_0.1.3            data.table_1.15.4         rtracklayer_1.64.0        prettyunits_1.2.0        
 [91] httr_1.4.7                htmlwidgets_1.6.4         S4Arrays_1.4.1            pkgconfig_2.0.3           gtable_0.3.5              blob_1.2.4               
 [97] siggenes_1.78.0           htmltools_0.5.8.1         ProtGenerics_1.36.0       scales_1.3.0              png_0.1-8                 knitr_1.48               
[103] rstudioapi_0.16.0         tzdb_0.4.0                rjson_0.2.21              nlme_3.1-164              checkmate_2.3.2           curl_5.2.1               
[109] org.Hs.eg.db_3.19.1       cachem_1.1.0              rhdf5_2.48.0              stringr_1.5.1             BiocVersion_3.19.1        foreign_0.8-86           
[115] AnnotationDbi_1.66.0      restfulr_0.0.15           GEOquery_2.72.0           pillar_1.9.0              grid_4.4.1                reshape_0.8.9            
[121] vctrs_0.6.5               dbplyr_2.5.0              xtable_1.8-4              cluster_2.1.6             htmlTable_2.4.3           evaluate_0.24.0          
[127] bsseq_1.40.0              readr_2.1.5               GenomicFeatures_1.56.0    cli_3.6.3                 compiler_4.4.1            Rsamtools_2.20.0         
[133] rngtools_1.5.2            rlang_1.1.4               crayon_1.5.3              nor1mix_1.3-3             mclust_6.1.1              interp_1.1-6             
[139] maftools_2.20.0           plyr_1.8.9                stringi_1.8.4             deldir_2.0-4              BiocParallel_1.38.0       munsell_0.5.1            
[145] lazyeval_0.2.2            Matrix_1.7-0              ExperimentHub_2.12.0      BSgenome_1.72.0           hms_1.1.3                 sparseMatrixStats_1.16.0 
[151] bit64_4.0.5               ggplot2_3.5.1             Rhdf5lib_1.26.0           KEGGREST_1.44.1           statmod_1.5.0             AnnotationHub_3.12.0     
[157] memoise_2.0.1             bit_4.0.5
missMethyl EPICv2manifest • 149 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States

You need to upgrade to the release version of Bioconductor. You have version 1.38.0 installed which indicates that you are using the previous release.

0
Entering edit mode

By version 1.38.0, I mean version 1.38.0 of MissMethyl.

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