[BioC] Illumina - Beadarray - Limma

[Lynn Amon]

Do you really need to do background subtraction with Illumina data?  Our 
experience is that this step is not necessary.

Lynn Amon
Research Scientist
University of Washington


Nieves Velez de Mendizabal wrote:
> 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
> 
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