[BioC] RobustSpline normalization method applied to agilent data

[Gordon K Smyth]

Dear Priscila,

You can't apply robust-spline normalization to an Agilent array. 
Robust-spline in limma is intended to moderate the loess curves over 
different print-tip groups.  But Agilent arrays don't have print-tips. 
For an Agilent arrays, only global loess normalization is meaningful, and 
that does not require the layout.

Best wishes
Gordon

> Date: Wed, 7 Mar 2012 09:16:22 -0300
> From: Priscila Grynberg <priscilag at gmail.com>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] RobustSpline normalization method applied to agilent
> 	data
>
> Dear BioCs,
>
> I received some agilent data to analyse using Limma, and I'm facing a
> problem when I tried to apply robustspline normalization within arrays
> method.
>
> ##Reading the files:
>
> RG = read.maimages(targets,,source="agilent", columns = list(G =
> "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal", Rb =
> "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum",
> "ControlType","ProbeName","SystematicName"))
>
> ##Background correction:
>
> RGn <- backgroundCorrect (RG, method="normexp", offset=50)
>
> #Normalization step
>
> MA <- normalizeWithinArrays(RGn, method="robustspline")
>
> Error in normalizeWithinArrays(RGn, method = "robustspline") :  Layout
> argument not specified
>
> ##Setting the printer information:
>
> nr <- length(unique(RG$genes$Row))
>
> nc <- length(unique(RG$genes$Col))
>
> RG$printer <- list(ngrid.r=1,ngrid.c=1,nspot.r=nr,nspot.c=nc)
>
> ## Trying again
>
> MA <- normalizeWithinArrays(RGn, RG$printer, method="robustspline")
>
> Error in X[O, ] <- ns(A[O], df = df, intercept = TRUE) : number of items to
> replace is not a multiple of replacement length
>
> I don't have the gal file like for this agilent slides. Can this be exactly
> the problem? Do you have any sugestions?
>
>
> Cheers,
>
> Priscila
>
>
> --
> Priscila Grynberg, D.Sc.- Bioinformatics
> Laboratório de Genética Bioquímica
> Universidade Federal de Minas Gerais
> Tel: +55 31 3409-2628
> CV: http://lattes.cnpq.br/8808643075395963

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