As I process both my own data and the example data, I am able to create an RGset (RGChannelSet object). However, an error occurs when I attempt to create a MethylSet object with any of the preprocess commands. The error is:
Error in `assayDataElement<-`(`*tmp*`, "Meth", validate = FALSE, value = c(22041, :
unused argument (validate = FALSE)
Here is my code (using the example data):
library(minfi)
library(minfiData)
baseDir <- system.file("extdata", package = "minfiData")
targets <- read.metharray.sheet(baseDir)
RGset <- read.metharray.exp(targets = targets)
rawset <- preprocessRaw(RGset)
Error in `assayDataElement<-`(`*tmp*`, "Meth", validate = FALSE, value = c(22041, :
unused argument (validate = FALSE)
traceback()
2: MethylSet(Meth = M, Unmeth = U, phenoData = phenoData(rgSet),
annotation = annotation(rgSet))
1: preprocessRaw(RGset)
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] minfiData_0.14.0
[2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
[3] IlluminaHumanMethylation450kmanifest_0.4.0
[4] minfi_1.19.13
[5] bumphunter_1.12.0
[6] locfit_1.5-9.1
[7] iterators_1.0.8
[8] foreach_1.4.3
[9] Biostrings_2.40.2
[10] XVector_0.12.1
[11] SummarizedExperiment_1.2.3
[12] GenomicRanges_1.24.3
[13] GenomeInfoDb_1.8.7
[14] IRanges_2.6.1
[15] S4Vectors_0.10.3
[16] lattice_0.20-34
[17] Biobase_2.32.0
[18] BiocGenerics_0.18.0
loaded via a namespace (and not attached):
[1] genefilter_1.54.2 splines_3.3.1
[3] beanplot_1.2 rtracklayer_1.32.2
[5] GenomicFeatures_1.24.5 chron_2.3-47
[7] XML_3.98-1.4 survival_2.39-5
[9] DBI_0.5-1 BiocParallel_1.6.6
[11] RColorBrewer_1.1-2 registry_0.3
[13] rngtools_1.2.4 doRNG_1.6
[15] matrixStats_0.50.2 plyr_1.8.4
[17] stringr_1.1.0 pkgmaker_0.22
[19] zlibbioc_1.18.0 codetools_0.2-14
[21] biomaRt_2.28.0 AnnotationDbi_1.34.4
[23] illuminaio_0.14.0 preprocessCore_1.34.0
[25] Rcpp_0.12.6 xtable_1.8-2
[27] openssl_0.9.4 limma_3.28.21
[29] base64_2.0 annotate_1.50.0
[31] Rsamtools_1.24.0 digest_0.6.10
[33] stringi_1.1.1 nor1mix_1.2-2
[35] grid_3.3.1 quadprog_1.5-5
[37] GEOquery_2.38.4 tools_3.3.1
[39] bitops_1.0-6 magrittr_1.5
[41] siggenes_1.46.0 RCurl_1.95-4.8
[43] RSQLite_1.0.0 MASS_7.3-45
[45] Matrix_1.2-7.1 data.table_1.9.6
[47] httr_1.2.1 reshape_0.8.5
[49] R6_2.1.3 mclust_5.2
[51] GenomicAlignments_1.8.4 multtest_2.28.0
[53] nlme_3.1-128
