How to format SWAN minfi data for bumphunter?
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Hello, I am analyzing Illumina 450K DNA methylation array data using the SWAN normalization procedures in minfi and I would like to use the statistical models in bumphunter. The bumphunter vignette indicates that data preprocessed in minfi can be used in bumphunter, however I am having difficulties formatting the SWAN-normalized minfi data properly. I successfully extracted the chr and pos to run clusterMaker. Below is the code of my attempt to get my minfi data formatted for bumphunter function. data<-getM(MSet.swan) #MethylSet of SWAN normalized data layout<-cbind(rep(1,12),rep(c(pd$Sample_Group))) #3 groups of 4 samples each, pd from pData in minfi #naming y from the vignette as data #naming X from the vignette as layout tab <- bumphunter(data, layout, chr, pos, clust, cutoff=.5) #Error in S %*% vv : requires numeric/complex matrix/vector arguments Any help would be much appreciated. -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] doRNG_1.5.3 [2] rngtools_1.2 [3] pkgmaker_0.16 [4] registry_0.2 [5] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3 [6] minfiData_0.3.2 [7] IlluminaHumanMethylation450kmanifest_0.4.0 [8] minfi_1.6.0 [9] Biostrings_2.28.0 [10] reshape_0.8.4 [11] plyr_1.8 [12] lattice_0.20-15 [13] Biobase_2.20.0 [14] bumphunter_1.0.0 [15] iterators_1.0.6 [16] foreach_1.4.1 [17] GenomicRanges_1.12.4 [18] IRanges_1.18.1 [19] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] beanplot_1.1 codetools_0.2-8 compiler_3.0.1 digest_0.6.3 [5] grid_3.0.1 illuminaio_0.2.0 itertools_0.1-1 limma_3.16.5 [9] MASS_7.3-26 matrixStats_0.8.1 mclust_4.1 multtest_2.16.0 [13] nor1mix_1.1-4 preprocessCore_1.22.0 RColorBrewer_1.0-5 R.methodsS3_1.4.2 [17] siggenes_1.34.0 splines_3.0.1 stats4_3.0.1 stringr_0.6.2 [21] survival_2.37-4 tools_3.0.1 xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.
minfi bumphunter minfi bumphunter • 940 views
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