Dear All, I a new in this kind of analyisis. I have to analyze some old data obtained with the technology: miRCURY LNA™ from Exiqon. I use routinely limma and lumi package to anlayze Illumina BeadChip microarray but is the first attempt to analyze data obtained form this platform. I used ExiMiR package for normalizing miRNA expression data and obtained an ExpressionSet object. > eset.spike ExpressionSet (storageMode: lockedEnvironment) assayData: 1988 features, 8 samples element names: exprs, se.exprs protocolData: none phenoData sampleNames: 1_Exiqon_14076908_S01_Cropped 1_Exiqon_14076910_S01_Cropped ... 0_Exiqon_14076913_S01_Cropped (8 total) varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: galenv.imagene.20140108105629478 I have 4 samples, 2 are control and 2 are cancer patients (Hy3 and Hy5) What I would like to do now is to use limma package to assess for differential expression between the two groups but I am really confused about dual color microarray and I can't proceed further without any hint, Could You please help me? Many Thanks, Paolo [[alternative HTML version deleted]]