[BioC] Weight functions for Agilent chips (limma)

[Giovanni Coppola]

Hi Joel,
actually, I was trying to use the 8 outlier fields (columns AZ-BG of the 
Agilent output file) in a way similar to the 'flag' fields of other platfoms...
So, I started with

mywtfun <- function(exclude.flags=c(1,2,3)) function(obj) 
1-(obj$rIsBGPopnOL %in% exclude.flags)
and thenRG <-read.maimages(...blabla... wt.fun=mywtfun(c(1)))

and maybe there's a way to include the other fields as well....
Any other ideas?

Cheers
Giovanni


At 02:56 PM 9/22/2004, Malard, Joel M wrote:
>Dear All,
>
>I was wondering what other people have been using for the weight
>function in read.maimages with Agilent arrays? I tried the following:
>
>wtAgilent.GFilter <- function(qta) { qta[,"gIsPosAndSignif"] }
>wtAgilent.RGFilter <- function(qta) {
>(qta[,"rIsPosAndSignif"]+qta[,"gIsPosAndSignif"])/2.0 }
>wtAgilent.RFilter <- function(qta) { qta[,"rIsPosAndSignif"] }
>wtAgilent.mRGFilter <- function(qta) {
>mapply(min,qta[,"gIsPosAndSignif"],qta[,"rIsPosAndSignif"]) }
>
>The last one seems to give somewhat "better results by-eye" when
>followed by loess normalization but is rather subjective.
>
>Best regards,
>
>Joel Malard
>
> >  -----Original Message-----
> > From:         Malard, Joel M
> > Sent: Friday, September 17, 2004 12:44 PM
> > To:   'bioconductor at stat.math.ethz.ch'
> > Subject:      Loess normalization for Agilent chips
> >
> >
> > I am struggling to get data from Agilent cDNA arrays into
> > BioConductor. It seems to me much easier to get the data in affy's
> > normalize.loess() than in the other cDNA array packages.
> >
> > Given that "one who get a bargain get what he pays for", does anyone
> > has comments, recommendations or warnings to share about using an Affy
> > normalization procedure on cDNA data?
> >
> > Thanks,
> >
> > Joel M. Malard, Ph.D.
> > Scientist IV
> > Pacific Northwest National Laboratory
> > Battelle Boulevard, PO Box 999
> > Mail Stop K1-85
> > Richland, WA 99352
> >
> > "I love the audacity of those who have everything to loose from it;
> > the moderation of those who have nothing to gain from it." Rostand,
> > Jean (1894-1977)
> >
> >
>
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>
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