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
>
>
> =
> =
> =
> =
> =
> =
> =
> =
> =
> =
> =
> =
> =
>
======================================================================
> L'Istituto Superiore di Sanit? (ISS) ? tra i beneficiari dei
> proventi del 5 per mille dell'IRPEF.
> Nella scheda allegata alla dichiarazione dei redditi ? sufficiente
> apporre la propria firma nel riquadro "Finanziamento della Ricerca
> Sanitaria" e indicare il Codice Fiscale dell'ISS, che ? 80211730587,
> per destinare tali fondi a sostegno dell'impegno scientifico
> dell'ISS a difesa della salute di tutti.
>
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----------------------------------------------------------------------
Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, M?nchen D
