Dear Gordon, Apologies should I have missed that this topic has already been discussed in the forum. We are using a small scale, custom made array containing 1760 features (440 probes in four replicates). Currently I am using the "loess" function in normalizeWithinArrays() for normalisation. I was wondering whether perhaps the "robustspline" function would be more appropriate but I am somewhat unclear what the differences between the two methods are and whether it would be suitable at all for our small scale arrays. Is there any more information available on that method other than already in the Limma user's guide? Thanks, Pie ------------------------------------- Dr Pie M?ller Vector Group Liverpool School of Tropical Medicine Pembroke Place Liverpool L3 5QA UK Tel +44(0) 151 705 3225 Fax +44(0) 151 705 3369 http://www.liv.ac.uk/lstm

At 11:37 PM 15/03/2007, Muller, Pie wrote: >Dear Gordon, > >Apologies should I have missed that this topic >has already been discussed in the forum. We are >using a small scale, custom made array >containing 1760 features (440 probes in four >replicates). Currently I am using the "loess" >function in normalizeWithinArrays() for >normalisation. I was wondering whether perhaps >the "robustspline" function would be more >appropriate but I am somewhat unclear what the >differences between the two methods are and >whether it would be suitable at all for our small scale arrays. robustspline is designed to be intermediate between "printtiploess" and "loess", depending on the data. It's not particularly aimed at small arrays, although it can cope with small print-tip groups in a way that printtiploess can't. The greater issue with with custom made arrays is whether your probes have been specially chosen so that more than half can be differentially expressed in a given situation. This issue is explored in http://genomebiology.com/2007/8/1/R2 One could argue that robustspline is a little more resistant to this than loess, but there's not much in it, see https://www.stat.math.ethz.ch/pipermail/bioconductor/2005-November/ 011006.html > Is there any more information available on > that method other than already in the Limma user's guide? No, the limma document is all that's available. Best wishes Gordon >Thanks, >Pie > >------------------------------------- > >Dr Pie M?ller >Vector Group >Liverpool School of Tropical Medicine >Pembroke Place >Liverpool >L3 5QA >UK > >Tel +44(0) 151 705 3225 >Fax +44(0) 151 705 3369 >http://www.liv.ac.uk/lstm