[BioC] how to use MethyLumiM object in BMIQ(wateRmelon)

[indranil [guest]]

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

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