[BioC] Illumina - Beadarray - Limma

[Nieves Velez de Mendizabal]

We are analyzing some data of Illumina. There are three kind of 
normalization. First of them is the method of rank invariant 
normalization, recommended by Illumina, and we would like to apply it:


    BSData.bgnorm = backgroundNormalise(BSData)
    T = apply(exprs(BSData.bgnorm), 1, mean)
    BSData.rankinv = assayDataElementReplace(BSData.bgnorm, "exprs",
    rankInvariantNormalise(exprs(BSData.bgnorm), T))


But in BSData.rankinv I have negative values so I cannot apply the 
method lmFit in order to analyze the differential expression because of 
the log2 transformation applied.

    fit = lmFit(log2(exprs(BSData.rankinv)), design)

Are these two methods (rank inv method and lmFit) incompatible?
What kind of normalization should I use in order to search 
differentially expressed genes in micro arrays of Illumina?

Thanks