List, I have illumina microarray data and I'm trying to use the lumi package to process it. I am running into some difficulties, and I am looking for suggestions on how to diagnose what is going wrong. # read in expression data fileName <- "samples.txt" myData <- lumiR(fileName) Duplicated IDs found and were merged! Perform Quality Control assessment of the LumiBatch object ... Warning messages: 1: In lumiR(fileName) : The data file may not be in the Illumia BeadStudio or GenomeStudio output format! 2: In matrix(as.double(exprs), nrow = nrow(allData)) : NAs introduced by coercion 3: In matrix(as.double(se.exprs), nrow = nrow(allData)) : NAs introduced by coercion 4: In matrix(as.double(detection), nrow = nrow(allData)) : NAs introduced by coercion 5: In matrix(as.double(beadNum), nrow = nrow(allData)) : NAs introduced by coercion # the names for the controls are not compatible with a data.frame so I had to change these. newNames <- paste("X",sampleNames(myData),sep="") newNames <- sub("-",".",newNames) sampleNames(myData) <- newNames # read in controls fileName <- "controls.txt" controls <- lumiR(fileName) Annotation columns are not available in the data. Duplicated IDs found and were merged! Perform Quality Control assessment of the LumiBatch object ... Warning message: In lumiR(fileName) : The data file may not be in the Illumia BeadStudio or GenomeStudio output format! # convert to data frame so I can add it to controlData slot controls <- exprs(controls) colnames(controls) <- paste("X",colnames(controls),sep="") controls <- data.frame(controls) myData at controlData <- controls lnormdata <- lumiB(myData,method='bgAdjust') Perform bgAdjust background correction ... # attempting VST, but having problems tryVST <- lumiT(lnormdata) Perform vst transformation ... 2011-11-17 16:34:50 , processing array 1 2011-11-17 16:34:50 , processing array 2 2011-11-17 16:34:50 , processing array 3 2011-11-17 16:34:50 , processing array 4 2011-11-17 16:34:51 , processing array 5 2011-11-17 16:34:51 , processing array 6 2011-11-17 16:34:51 , processing array 7 2011-11-17 16:34:51 , processing array 8 2011-11-17 16:34:51 , processing array 9 2011-11-17 16:34:51 , processing array 10 2011-11-17 16:34:51 , processing array 11 2011-11-17 16:34:51 , processing array 12 Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases In addition: Warning messages: 1: In lumiT(lnormdata) : Too few probes are detectable based on detection p-values! Iteration method will be used for VST. 2: In lumiT(lnormdata) : Too few probes are detectable based on detection p-values! Iteration method will be used for VST. 3: In lumiT(lnormdata) : Too few probes are detectable based on detection p-values! Iteration method will be used for VST. Can anyone suggest how to diagnose what is going wrong? Thanks for your help. In case it is useful at all, the beginning of the file looks like. [Sample Probe Profile] PROBE_ID SYMBOL 262-00715.AVG_Signal 262-00715.NARRAYS 262-00715.ARRAY_STDEV 262-00715.BEAD_STDERR 262-00715.Avg_NBEADS > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.6.0 nleqslv_1.9.0 methylumi_2.0.1 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affy_1.32.0 affyio_1.22.0 annotate_1.32.0 [4] AnnotationDbi_1.16.2 BiocInstaller_1.2.1 DBI_0.2-5 [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.1 [10] KernSmooth_2.23-7 lattice_0.20-0 MASS_7.3-16 [13] Matrix_1.0-1 mgcv_1.7-11 nlme_3.1-102 [16] preprocessCore_1.16.0 RSQLite_0.10.0 xtable_1.6-0 [19] zlibbioc_1.0.0