Z!™™™ On Jul 16, 2010 2:32 PM, "Wolfgang Huber" <whuber@embl.de> wrote: Ning I assume you are refering to the normalizePlates function in the cellHTS2 package. (Please don't forget in the future to provide such information, and also sessionInfo(), this is much better than letting us guess.) There are two answers to your question: 1. You can use the 'assayData' accessor to read from or write to the data slot. For instance: library("cellHTS2") datadir = system.file("KcViabSmall", package = "cellHTS2") x = readPlateList("Platelist.txt", "KcViabSmall", path=datadir) class(x) ls(assayData(x)) head(assayData(x)$"Channel 1") if(storageMode(assayData(x))=="lockedEnvironment") storageMode(assayData(x)) = "environment" assayData(x)$"Channel 1" = assayData(x)$"Channel 1" * pi/2 /* Background: The function 'normalizePlates' takes an object of class 'cellHTS2' with raw readings as input and returns one with normalised data as a result. The class 'cellHTS2' derives from 'NChannelSet', which is a common Bioconductor class for matrix-like data plus all relevant metadata. */ 2. You can have a look at the source code of 'normalizePlates' (which is simply a wrapper to call one of the specific normalization methods selected by the argument "method") and copy/edit it to a new function that calls your favorite normalization function instead. Best wishes Wolfgang On Jul/8/10 10:08 PM, Ning wrote: > > Hi everyone, > > The cellHTS2 method normalizePlates has n... -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.e... [[alternative HTML version deleted]]