Hi There, I am using normalizeWithinArrays function from the limma package for a within array normalization . There were no missing/NA values in the input data file, however, after the within array normalization, there are some of NA values in the M file , I wonder under which condition the function returns NA to M ? How can I do a between array normalization based on the within array normalized data which has some NA values? FYI - My data is aCGH data from Agilent, the normalization method I used was loess . thank you very much! I am looking forward to hearing back from you! Joan Zhang [[alternative HTML version deleted]]

It has nothing to do with the normalization method. See ?backgroundCorrect and the bc.method argument to normalizeWithinArrays. Gordon > Date: Thu, 2 Aug 2012 13:42:53 -0500 > From: "Zhang, Xueqiong" <xueqiong.zhang at="" vanderbilt.edu=""> > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] limma - NA values after withinarray normalization > > Hi There, > I am using normalizeWithinArrays function from the limma package for a > within array normalization . There were no missing/NA values in the > input data file, however, after the within array normalization, there > are some of NA values in the M file , I wonder under which condition the > function returns NA to M ? How can I do a between array normalization > based on the within array normalized data which has some NA values? > FYI - My data is aCGH data from Agilent, the normalization method I > used was loess . > > thank you very much! > > I am looking forward to hearing back from you! > > Joan Zhang > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}