Hi all, I must admit that I am quite new to both methylation data analysis and R. I am currently analyzing IlluminaHumanMethylation450k array. Before using BMIQ method I have used lumi package to perform a background correction and created a MethyLumiM object. Is it possible to use MethyLumiM object as input in BMIQ method? When I try to use it, I got following error: > BMIQ.AvgBeta_24=BMIQ(AvgBeta_24, nfit=100) Error in BMIQ(AvgBeta_24, nfit = 100) : argument "design.v" is missing, with no default In addition: Warning message: In is.na(beta.v) : is.na() applied to non-(list or vector) of type 'S4' However if I use methylumi package to load my data which creates a MethyLumiSet object, BMIQ is working fine with me. Please suggest me if there is any alternative way to use MethyLumiM object as input for BMIQ method. Below I am attaching the description of both the objects. Thanks for your help. > AvgBeta_24 MethyLumiM (storageMode: lockedEnvironment) assayData: 485577 features, 24 samples element names: detection, exprs, methylated, unmethylated protocolData: none phenoData sampleNames: BEA1_NGT BEA13_T2DM ... BEA24_Lean (24 total) varLabels: sampleID label varMetadata: labelDescription featureData featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total) fvarLabels: Index TargetID ... POSITION (8 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: > AvgBeta_methylumi Object Information: MethyLumiSet (storageMode: lockedEnvironment) assayData: 485577 features, 24 samples element names: betas, Intensity, methylated, pvals, unmethylated protocolData: none phenoData sampleNames: BEA1_NGT BEA13_T2DM ... BEA24_Lean (24 total) varLabels: sampleID label varMetadata: labelDescription featureData featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total) fvarLabels: Index TargetID ... ProbeID_B (6 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: Major Operation History: submitted finished 1 2013-04-16 09:15:46 2013-04-16 09:17:03 command 1 methylumiR(filename = "Avg_Beta_values_24samples.txt", lib = "IlluminaHumanMethylation450k.db") Best regards, Indranil. -- output of sessionInfo(): > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 [4] LC_NUMERIC=C LC_TIME=Swedish_Sweden.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] wateRmelon_1.0.0 ROC_1.36.0 IlluminaHumanMethylation450k.db_2.0.7 [4] org.Hs.eg.db_2.9.0 RSQLite_0.11.2 DBI_0.2-5 [7] AnnotationDbi_1.22.1 lumi_2.12.0 matrixStats_0.6.2 [10] limma_3.16.1 RPMM_1.10 cluster_1.14.4 [13] BiocInstaller_1.10.0 methylumi_2.6.1 ggplot2_0.9.3.1 [16] reshape2_1.2.2 scales_0.2.3 Biobase_2.20.0 [19] BiocGenerics_0.6.0 loaded via a namespace (and not attached): Error in x[["Version"]] : subscript out of bounds In addition: Warning message: In FUN(c("affy", "affyio", "annotate", "beanplot", "Biostrings", : DESCRIPTION file of package 'colorspace' is missing or broken -- Sent via the guest posting facility at bioconductor.org.