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, M?nchen D