I have data from Agilent Human miRNA Microarray Version3 chips which were extracted using FeatureExtractor 10.5.1.1. When trying to invoke readMicroRnaAFE on these files I get the following error: dd.micro = readMicroRnaAFE(targets.micro, verbose=TRUE) Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file It seems like column Rb = "gMeanSignal" is missing in my data. Is it ok to use gMedianSignal instead? Furthermore dd$genes = ddaux$genes[, c(4, 5, 6)] makes problems, as ddaux$genes has only 5 columns Row, Col, ControlType, ProbeName, SystematicName The first lines of one of my input files: integer integer text text float float float float float float float boolean boolean boolean boolean boolean boolean boolean float boolean boolean float float float float float float boolean SubTypeMask ControlType ProbeName SystematicName PositionX PositionY gProcessedSignal gProcessedSigError gMedianSignal gBGMedianSignal gBGPixSDev gIsSaturated gIsLowPMTScaledUp gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gIsPosAndSignif gIsWellAboveBG SpotExtentX gBGMeanSignal gTotalProbeSignal gTotalProbeError gTotalGeneSignal gTotalGeneError gIsGeneDetected 0 1 miRNABrightCorner30 miRNABrightCorner30 413121 211.44 2.205295e+002 2.228109e+001 305 48 9.292912e+000 0 0 0 0 0 0 0 220.53 1 1 53.5237 49.2325 112972 11.5848 112972 11.5848 1 66 1 DarkCorner DarkCorner 438727 212104 4.665936e+000 3.214336e+000 79 50 9.037640e+000 0 0 0 0 1 0 0 4.66594 1 0 49.1849 50.1741 2.20202 5.44024 2.20202 5.44024 0 > sessionInfo() R version 2.11.0 RC (2010-04-19 r51778) x86_64-pc-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.0 [4] limma_3.4.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 Thanks for your help, Christian