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List:       bioconductor
Subject:    [BioC] Agi4x44PreProcess probe summarization bug?
From:       Tobias Straub <tstraub () med ! uni-muenchen ! de>
Date:       2009-06-28 15:16:25
Message-ID: 634EBBCA-4A7A-4FCA-8B4E-CA191BA696EC () med ! uni-muenchen ! de
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Hi Pedro,

i checked out the summarize.probe function in Agi4x44PreProcess. i  
might be mistaken, but it looks as if this function does not do what  
you describe. looking at the source code, it rather looks as if you  
calculate the median but you never write it into the new RGList. in  
fact, the collapsed list contains the values of the top index probe  
and not the median of all probes.

here the code snippet. ddPROC does never get the MED values, as far as  
i understand the code.
####

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

###

I am referring to Version 1.4.0 of Agi4x44PreProcess


best regards
Tobias

----------------------------------------------------------------------
Tobias Straub   ++4989218075439   Adolf-Butenandt-Institute, München D

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