Hi Tom I believe it is because your data doesn¹t include the ³BEAD_STD² columns, which is required for the LumiBatch class. So please ask your data provider include the ³BEAD_STD² columns. If not, please just go ahead and use log2 transformation instead of ³vst² transformation. All other procedures are the same. Pan On 1/27/11 7:09 AM, "Thomas Hampton" <thomas.h.hampton@dartmouth.edu> wrote: > > > 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. For example, I can't perform QC... > > > 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 >> > > Thanks very much for any advice, > > Tom [[alternative HTML version deleted]]