[BioC] Agi4x44PreProcess probe summarization bug?

[Tobias Straub]

Hi Massimo,

in principle the effect should not be dramatic if the replicate  
signals are not too different. it's rather easy to correct the  
function by overriding it with the correct code. this is my quick fix,  
not tested at all.
have a look and try it out.

best
Tobias

######

`summarize.probe` <-
function(ddFILT,makePLOT,targets) {

	cat("SUMMARIZATION OF non-CTRL PROBES ","\n")
	cat("\n")
	if (!is(ddFILT, "RGList")){
	  stop("'input' must be a RGList")
   	 	if (is.null(dim(ddFILT)[1])) {
        		stop("'input' is empty")
	 	}
	}

	if(missing(targets)){
		stop("'targets' is missing ")
	}

	if("GErep" %in% colnames(targets)){
		GErep=targets$GErep
		nGE=sum(table(table(GErep)))
	}else{
		stop("'targets' needs 'GErep' field")
	}
		
	ddDUP=ddFILT
	dup=which(duplicated(ddDUP$genes$ProbeName)==TRUE)

		if(length(dup) == 0){
			ddPROC=ddFILT
			stop("NOT DUPLICATED ProbeName in chip")
			}

	
	Ldup=length(dup)
	reps=table(ddDUP$genes$ProbeName[dup])
	t=table(reps)
	rN=names(reps)
	Lreps=length(rN)
	
	nARR=dim(ddDUP)[2]

	if(Lreps !=0){
		for(i in 1:Lreps){
  			index=which(ddDUP$genes$ProbeName==rN[i])
  			MED=apply(ddDUP$G[index,],2,median)
  			for (k in 1:length(index)) {
  				ddDUP$G[index,][k,] <- MED
  			}
		}
		ddPROC=ddDUP[-dup,]
	} else{
		ddPROC=ddDUP
	}

		# cat("REPLICATED NonCtrl",Lreps,"\n")
		# cat("DISTRIBUTION OF REPLICATED NonControl Probes","\n")
		# print(t)
		# cat("# REPLICATED (redundant) probeNames",Ldup,"\n")
		# cat("\n")
		cat("SUMMARIZED DATA: ",dim(ddPROC),"\n")
		cat("------------------------------------------------------","\n")

	
	if(!missing(makePLOT)) {
	if(makePLOT){
	
	colorfill="green"		
	maintitle="NORMALIZED & SUMMARIZED SIGNAL"

	X11()
	par(mfrow=c(1,1))
	plotDensity(ddPROC$G,maintitle)

	X11()
	par(mfrow=c(1,1))
	BoxPlot(ddPROC$G,maintitle,colorfill)

	X11()
	maintitle="NORMALIZED & SUMMARIZED DATA - RLE "
	RLE(ddPROC$G,maintitle,colorfill)

	X11()
	par(mfrow=c(2,2),ask=T)
	maintitle="summ data"
	MVAplotMED(ddPROC$G,colorfill,maintitle)

	X11()
	par(mfrow=c(1,1))
	hierclus(ddPROC$G,GErep,methdis="euclidean",
        methclu="complete",sel=FALSE,100)

	}
	}

return(ddPROC)
} # end function

#####

On Aug 4, 2009, at 2:18 PM, Massimo Pinto wrote:

> Hi Tobias,
> I am trying to figure out what would be the effect of this potential  
> bug. Have you tried to correct the function to see what happens when  
> MED is returned?
> Massimo
>
> -- 
> Massimo Pinto
> Post Doctoral Research Fellow
> Enrico Fermi Centre and Italian Public Health Research Institute  
> (ISS), Rome
> http://claimid.com/massimopinto
>
>
> = 
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----------------------------------------------------------------------
Tobias Straub   ++4989218075439   Adolf-Butenandt-Institute, München D