[BioC] Spot Quality Weights for Agilent arrays

Francesca Guana francesca.guana at tiscali.it
Thu Sep 8 12:33:38 CEST 2005

```Dear All,

I'm a beginner with R and I need some help. I have some Agilent oligo arrays
to analyze. I would like to know a good way to assign spot weights or to
do some spot quality  control using read.maimages() within limma package.
I found some suggestion about some weight finctions in the Bioconductor archive

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"]) }

wtAgilent.mRGOLFilter <- function(qta) {
mapply(min,1-qta[,"gIsFeatNonUnifOL"],1-qta[,"gIsFeatNonUnifOL"],
1-qta[,"gIsBGNonUnifOL"],1-qta[,"gIsBGNonUnifOL"],
1-qta[,"gIsFeatPopnOL"],1-qta[,"gIsFeatPopnOL"],
1-qta[,"gIsBGPopnOL"],1-qta[,"gIsBGPopnOL"])
}

Are there any less "drastic" ways to consider spots which for some reason
are considered as outliers? Does it make some sense assigning weights not
equal to zero for these outliers? Which can be a good criteria to assign
these weights?

Best regards
Francesca

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