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 __________________________________________________________________ TISCALI ADSL 1.25 MEGA Solo con Tiscali Adsl navighi senza limiti e telefoni senza canone Telecom a partire da 19,95 Euro/mese. Attivala entro il 31 agosto, il primo MESE ? GRATIS! CLICCA QUI. http://abbonati.tiscali.it/adsl/sa/1e25flat_tc/