Entering edit mode
Hello,
I am running my R script for the analysis of some EPIC array data and I have encountered an error in some of the last lines of the script which I am really struggling to move past and I'm wondering if you have any suggestions to help - I really appreciate it :)
I just don't really understand where to route the error back to
Kind regards, Grace
Code should be placed in three backticks as shown below
#
> fit <- lmFit(MSw, design)
Error in lmFit(MSw, design) : design must be a numeric matrix
# please also include the results of running the following in an R session
sessionInfo( )
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8
[2] LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ggplot2_3.4.0
[2] circlize_0.4.15
[3] reshape2_1.4.4
[4] corpcor_1.6.10
[5] CpGassoc_2.60
[6] data.table_1.14.6
[7] qqman_0.1.8
[8] tidyr_1.2.1
[9] pvclust_2.2-0
[10] sqldf_0.4-11
[11] RSQLite_2.2.20
[12] gsubfn_0.7
[13] proto_1.0.0
[14] pcaMethods_1.90.0
[15] sva_3.46.0
[16] BiocParallel_1.32.5
[17] genefilter_1.80.3
[18] mgcv_1.8-41
[19] nlme_3.1-160
[20] dplyr_1.0.10
[21] limma_3.54.0
[22] WGCNA_1.72-1
[23] fastcluster_1.2.3
[24] dynamicTreeCut_1.63-1
[25] GO.db_3.16.0
[26] AnnotationDbi_1.60.0
[27] missMethyl_1.32.0
[28] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[29] MatrixEQTL_2.3
[30] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
[31] IlluminaHumanMethylation450kmanifest_0.4.0
[32] FlowSorted.Blood.EPIC_2.2.0
[33] ExperimentHub_2.6.0
[34] AnnotationHub_3.6.0
[35] BiocFileCache_2.6.0
[36] dbplyr_2.3.0
[37] FlowSorted.Blood.450k_1.36.0
[38] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[39] IlluminaHumanMethylationEPICmanifest_0.3.0
[40] minfi_1.44.0
[41] bumphunter_1.40.0
[42] locfit_1.5-9.7
[43] iterators_1.0.14
[44] foreach_1.5.2
[45] Biostrings_2.66.0
[46] XVector_0.38.0
[47] SummarizedExperiment_1.28.0
[48] Biobase_2.58.0
[49] MatrixGenerics_1.10.0
[50] matrixStats_0.63.0
[51] GenomicRanges_1.50.2
[52] GenomeInfoDb_1.34.6
[53] IRanges_2.32.0
[54] S4Vectors_0.36.1
[55] BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 tidyselect_1.2.0
[3] htmlwidgets_1.6.1 grid_4.2.2
[5] munsell_0.5.0 codetools_0.2-18
[7] preprocessCore_1.60.2 chron_2.3-58
[9] interp_1.1-3 statmod_1.5.0
[11] withr_2.5.0 colorspace_2.0-3
[13] filelock_1.0.2 knitr_1.41
[15] rstudioapi_0.14 GenomeInfoDbData_1.2.9
[17] bit64_4.0.5 rhdf5_2.42.0
[19] vctrs_0.5.1 generics_0.1.3
[21] xfun_0.36 R6_2.5.1
[23] doParallel_1.0.17 illuminaio_0.40.0
[25] bitops_1.0-7 rhdf5filters_1.10.0
[27] cachem_1.0.6 reshape_0.8.9
[29] DelayedArray_0.23.2 assertthat_0.2.1
[31] promises_1.2.0.1 BiocIO_1.8.0
[33] scales_1.2.1 nnet_7.3-18
[35] gtable_0.3.1 rlang_1.0.6
[37] calibrate_1.7.7 GlobalOptions_0.1.2
[39] splines_4.2.2 rtracklayer_1.58.0
[41] impute_1.72.3 GEOquery_2.66.0
[43] checkmate_2.1.0 BiocManager_1.30.19
[45] yaml_2.3.6 GenomicFeatures_1.50.3
[47] backports_1.4.1 httpuv_1.6.8
[49] Hmisc_4.7-2 tcltk_4.2.2
[51] tools_4.2.2 nor1mix_1.3-0
[53] ellipsis_0.3.2 RColorBrewer_1.1-3
[55] siggenes_1.72.0 Rcpp_1.0.9
[57] plyr_1.8.8 base64enc_0.1-3
[59] sparseMatrixStats_1.10.0 progress_1.2.2
[61] zlibbioc_1.44.0 purrr_1.0.1
[63] RCurl_1.98-1.9 prettyunits_1.1.1
[65] rpart_4.1.19 openssl_2.0.5
[67] deldir_1.0-6 cluster_2.1.4
[69] magrittr_2.0.3 hms_1.1.2
[71] mime_0.12 xtable_1.8-4
[73] XML_3.99-0.13 jpeg_0.1-10
[75] mclust_6.0.0 shape_1.4.6
[77] gridExtra_2.3 compiler_4.2.2
[79] biomaRt_2.54.0 tibble_3.1.8
[81] crayon_1.5.2 htmltools_0.5.4
[83] later_1.3.0 tzdb_0.3.0
[85] Formula_1.2-4 DBI_1.1.3
[87] MASS_7.3-58.1 rappdirs_0.3.3
[89] Matrix_1.5-1 readr_2.1.3
[91] cli_3.6.0 quadprog_1.5-8
[93] pkgconfig_2.0.3 GenomicAlignments_1.34.0
[95] foreign_0.8-83 xml2_1.3.3
[97] annotate_1.76.0 rngtools_1.5.2
[99] multtest_2.54.0 beanplot_1.3.1
[101] doRNG_1.8.6 scrime_1.3.5
[103] stringr_1.5.0 digest_0.6.31
[105] base64_2.0.1 htmlTable_2.4.1
[107] edgeR_3.40.2 DelayedMatrixStats_1.20.0
[109] restfulr_0.0.15 curl_5.0.0
[111] shiny_1.7.4 Rsamtools_2.14.0
[113] rjson_0.2.21 lifecycle_1.0.3
[115] Rhdf5lib_1.20.0 askpass_1.1
[117] fansi_1.0.3 pillar_1.8.1
[119] lattice_0.20-45 KEGGREST_1.38.0
[121] fastmap_1.1.0 httr_1.4.4
[123] survival_3.4-0 interactiveDisplayBase_1.36.0
[125] glue_1.6.2 png_0.1-8
[127] BiocVersion_3.16.0 bit_4.0.5
[129] stringi_1.7.12 HDF5Array_1.26.0
[131] blob_1.2.3 org.Hs.eg.db_3.16.0
[133] latticeExtra_0.6-30 memoise_2.0.1
