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 > [[alternative HTML version deleted]]