Dear Sally, Here are two pieces of advice which apply generally to most functions in Bioconductor or R, and certainly to limma. Firstly, tuning arguments are usually set to default values which are sensible for most purposes. You would have to have a special reason for choosing something different. You have not mentioned any reason why the default settings of normalizeWithinArrays are not suitable for you. Secondly, if you want to learn more, you read the help page for that function and follow the references given. In this case, ?normalizeWithinArrays The 3rd reference looks especially relevant. BTW, reading the help page would tell you that the 'df' argument is not used for loess normalization. Best wishes Gordon >Date: Wed, 24 Oct 2007 18:28:19 -0700 >From: Sally <sagoldes at="" shaw.ca=""> >Subject: [BioC] Arguments for normalizewithinarrays (Limma) >To: bioconductor at stat.math.ethz.ch > >I am trying to understand what values I should put in for the >following arguments. For example how many iterations should I >use. What is a good value for span, df etc.? Can anyone guide >me? Is there a good reference source for this information? > >normalizeWithinArrays(object, layout, method="printtiploess", >weights=object$weights, span=0.3, iterations=4, controlspots=NULL, >df=5, robust="M", bc.method="subtract", offset=0)