[BioC] RobustSpline normalization method applied to agilent data

[sylvia]

Priscila Grynberg <priscilag at ...> writes:

> 
> Dear Gordon,
> 
> Thanks for the explanation. I didnt realize robust spline was dependent of
> print-tips.
> 
> Sincerely,
> 
> Priscila
> 
Dear all,

I also applied the robust spline with the Agilent two colour array data, 
however, I did not get any errors.... are the error messages depend on the 
package that I use?

This is what I did:

targets        <- readTargets(file = cfg$target.files);

RG <- read.maimages(
	files = targets$FileName,
	source = "agilent",
	columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = 
"rMedianSignal", Rb = "rBGMedianSignal"),
	annotation = c("Row", "Col", "FeatureNum", "ControlType", "ProbeName", 
"GeneName")
	);

 RG <- backgroundCorrect(RG, method="minimum", offset=1)
 MA <- normalizeWithinArrays(RG, method="robustspline")


### Session Info 
################################################################################
###
R version 2.14.2 (2012-02-29)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] splines   grid      stats     graphics  grDevices datasets  methods  
[8] utils     base     

other attached packages:
MASS_7.3-17     
latticeExtra_0.6-19                 
lattice_0.20-0                      
limma_3.10.3    









> On Thursday, March 8, 2012, Gordon K Smyth <smyth at ...> wrote:
> > 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 ...>
> >> To: <bioconductor at ...>
> >> 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
> >
> > ______________________________________________________________________
> > The information in this email is confidential and inte...{{dropped:12}}
> 
> 
> 
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