[BioC] Weight functions for Agilent chips (limma)

Malard, Joel M JM.Malard at pnl.gov
Wed Sep 22 23:56:28 CEST 2004

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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