As I think you can see below, my call to lumiR, which is meant to  
create a LumiBatch,
instead creates an expression set. This is not the same animal as a  
LumiBatch, so I am
sort of stuck.


data <- lumiR("FinalReport.txt", lib.mapping = "lumiHumanIDMapping")
 > data
ExpressionSet (storageMode: lockedEnvironment)
assayData: 47231 features, 24 samples
   element names: detection, exprs
protocolData: none
phenoData
   sampleNames: 5713430005_A 5713430005_B ... 5713430009_L (24 total)
   varLabels: sampleID
   varMetadata: labelDescription
featureData
   featureNames: Ku8QhfS0n_hIOABXuE fqPEquJRRlSVSfL.8A ...
     N8t5EuJCr0Tk9.zHno (47231 total)
   fvarLabels: ProbeID TargetID ... DEFINITION (9 total)
   fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: lumiHumanAll.db

 > dim(exprs(data))
[1] 47231    24



 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] lumiHumanAll.db_1.12.0   org.Hs.eg.db_2.4.6        
lumiHumanIDMapping_1.8.0
[4] RSQLite_0.9-4            DBI_0.2-5                 
AnnotationDbi_1.12.0
[7] lumi_2.3.1               Biobase_2.10.0           limma_3.6.9

loaded via a namespace (and not attached):
  [1] affy_1.28.0           affyio_1.18.0         annotate_1.28.0
  [4] grid_2.12.0           hdrcde_2.15           KernSmooth_2.23-4
  [7] lattice_0.19-13       MASS_7.3-8            Matrix_0.999375-44
[10] methylumi_1.6.1       mgcv_1.6-2            nlme_3.1-97
[13] preprocessCore_1.12.0 xtable_1.5-6
 >


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