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

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