[BioC] How to format SWAN minfi data for bumphunter?

[Lara Park [guest]]

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   

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