Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
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pcibin • 0
@1f5797b3
Last seen 10 days ago
Germany

Hey everyone,

I am working with data from the Epicv2 and I want to use several graphical interfaces to look at my data. I started by using ShinyMethyl and that worked without problem after I specify the array and manifest in the RGset.

RGset = minfi::read.metharray.exp(targets = samplesheet_1, verbose = TRUE, extended = TRUE)
#1.  Update the annotation package to hg38 coordinates for the Epicv2 from here: <https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38>
# https://github.com/jokergoo/IlluminaHumanMethylationEPICv2manifest
annotation(RGset)
annotation(RGset)["array"] = "IlluminaHumanMethylationEPICv2"
annotation(RGset)["annotation"] = "20a1.hg38"
annotation(RGset)
shinyRGset_raw <- shinySummarize(object = RGset)

Problem is, when I tried to run MethylAid i get the following

> methAidData_raw <- MethylAid::summarize(samplesheet_1, file=RGset)
Start summarization ...
Summarize data in one go...
Error in .getManifestString(object@annotation) : 
Cannot get Manifest object for an 'Unknown' array

Now, I am a beginner in this, but I suppose that the problem is that since the input is the samplesheet, MethylAid doesn't have the array, manifest and annotation information. How can I specify it? Since both packages are minfi based, it should be possible I guess?

sessionInfo( )
R version 4.3.2 (2023-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

Matrix products: default
BLAS/LAPACK: /gnu/store/in3yw5xrghzmxn29i0mmz5zhpd748mas-openblas-0.3.20/lib/libopenblasp-r0.3.20.so;  LAPACK version 3.9.0

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       

time zone: UTC+1
tzcode source: system (glibc)

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

other attached packages:
 [1] MethylAid_1.36.0                                   BiocManager_1.30.22                               
 [3] ewastools_1.7.2                                    shiny_1.8.0                                       
 [5] IlluminaHumanMethylationEPICv2manifest_1.0.0       shinyMethyl_1.38.0                                
 [7] IlluminaHumanMethylationEPICv2anno.20a1.hg38_1.0.0 minfi_1.48.0                                      
 [9] bumphunter_1.44.0                                  locfit_1.5-9.8                                    
[11] iterators_1.0.14                                   foreach_1.5.2                                     
[13] Biostrings_2.70.1                                  XVector_0.42.0                                    
[15] SummarizedExperiment_1.32.0                        Biobase_2.62.0                                    
[17] MatrixGenerics_1.14.0                              matrixStats_1.2.0                                 
[19] GenomicRanges_1.54.1                               GenomeInfoDb_1.38.5                               
[21] IRanges_2.36.0                                     S4Vectors_0.40.2                                  
[23] BiocGenerics_0.48.1                                IlluminaHumanMethylationEPICmanifest_1.0.0        
[25] devtools_2.4.5                                     usethis_2.2.2                                     
[27] stringr_1.5.1                                      dplyr_1.1.4                                       

loaded via a namespace (and not attached):
  [1] splines_4.3.2             later_1.3.2               BiocIO_1.12.0             bitops_1.0-7             
  [5] filelock_1.0.3            tibble_3.2.1              preprocessCore_1.64.0     XML_3.99-0.16            
  [9] lifecycle_1.0.4           processx_3.8.3            lattice_0.22-5            MASS_7.3-60              
 [13] base64_2.0.1              scrime_1.3.5              magrittr_2.0.3            limma_3.58.1             
 [17] sass_0.4.8                rmarkdown_2.25            jquerylib_0.1.4           yaml_2.3.8               
 [21] remotes_2.4.2.1           httpuv_1.6.13             doRNG_1.8.6               askpass_1.2.0            
 [25] sessioninfo_1.2.2         pkgbuild_1.4.3            DBI_1.2.0                 RColorBrewer_1.1-3       
 [29] abind_1.4-5               pkgload_1.3.3             quadprog_1.5-8            purrr_1.0.2              
 [33] RCurl_1.98-1.13           rappdirs_0.3.3            GenomeInfoDbData_1.2.0    genefilter_1.84.0        
 [37] annotate_1.80.0           DelayedMatrixStats_1.24.0 codetools_0.2-19          DelayedArray_0.28.0      
 [41] xml2_1.3.6                tidyselect_1.2.0          beanplot_1.3.1            BiocFileCache_2.10.1     
 [45] illuminaio_0.44.0         GenomicAlignments_1.38.0  jsonlite_1.8.8            multtest_2.58.0          
 [49] ellipsis_0.3.2            survival_3.5-7            systemfonts_1.0.5         tools_4.3.2              
 [53] progress_1.2.3            ragg_1.2.7                Rcpp_1.0.11               glue_1.6.2               
 [57] SparseArray_1.2.3         xfun_0.41                 HDF5Array_1.30.0          withr_2.5.2              
 [61] fastmap_1.1.1             rhdf5filters_1.14.1       fansi_1.0.6               openssl_2.1.1            
 [65] callr_3.7.3               digest_0.6.33             R6_2.5.1                  mime_0.12                
 [69] colorspace_2.1-0          textshaping_0.3.7         biomaRt_2.58.0            RSQLite_2.3.4            
 [73] hexbin_1.28.3             utf8_1.2.4                tidyr_1.3.0               generics_0.1.3           
 [77] data.table_1.14.10        rtracklayer_1.62.0        prettyunits_1.2.0         httr_1.4.7               
 [81] htmlwidgets_1.6.4         S4Arrays_1.2.0            pkgconfig_2.0.3           gtable_0.3.4             
 [85] blob_1.2.4                siggenes_1.76.0           htmltools_0.5.7           profvis_0.3.8            
 [89] scales_1.3.0              png_0.1-8                 knitr_1.45                rstudioapi_0.15.0        
 [93] tzdb_0.4.0                rjson_0.2.21              nlme_3.1-164              curl_5.2.0               
 [97] cachem_1.0.8              rhdf5_2.46.1              miniUI_0.1.1.1            AnnotationDbi_1.64.1     
[101] restfulr_0.0.15           desc_1.4.3                GEOquery_2.70.0           pillar_1.9.0             
[105] grid_4.3.2                reshape_0.8.9             vctrs_0.6.5               urlchecker_1.0.1         
[109] promises_1.2.1            dbplyr_2.4.0              xtable_1.8-4              evaluate_0.23            
[113] readr_2.1.4               GenomicFeatures_1.54.1    cli_3.6.2                 compiler_4.3.2           
[117] Rsamtools_2.18.0          rlang_1.1.2               crayon_1.5.2              rngtools_1.5.2           
[121] nor1mix_1.3-2             mclust_6.0.1              ps_1.7.5                  plyr_1.8.9               
[125] fs_1.6.3                  stringi_1.8.3             gridBase_0.4-7            BiocParallel_1.36.0      
[129] munsell_0.5.0             Matrix_1.6-4              hms_1.1.3                 sparseMatrixStats_1.14.0 
[133] bit64_4.0.5               ggplot2_3.4.4             Rhdf5lib_1.24.1           KEGGREST_1.42.0          
[137] statmod_1.5.0             memoise_2.0.1             bslib_0.6.1               bit_4.0.5
minfi EPICv2manifest MethylAid • 103 views
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