[BioC] RobustSpline normalization method applied to agilent data

[Heidi Dvinge]

Hi Priscilla,

> 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))
>
Does the number of spots in your file actually equal nr*nc? Sometimes GAL
files for Agilent doesn't contain entries for spots on the array where
nothing has been printed.

If you look at the combinations of RG$genes$Row and RG$genes$Col in your
file, you may find that some of them are missing. If so, you will perhaps
need to add some dummy values manually in order to use robustspline.

HTH
\Heidi

> RG$printer <- list(ngrid.r=1,ngrid.c=1,nspot.rr,nspot.cc)
>
> ## Trying again
>
> MA <- normalizeWithinArrays(RGn, RG$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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>
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