I have committed a new function avereps() in the limma package on Bioconductor. It is somewhat slow, but will handle irregularly spaced spots. I have committed it to both the release and developmental branches of Bioconductor. If you re-install limma from Bioconductor in a couple days you should be able to use it. Best wishes Gordon On Tue, 3 Jun 2008, Erika Melissari wrote: > Dear Dr Smyth, > > I am a PhD student at University of Pisa. > I frequently use LIMMA package to handle gene expression microarray data. > I have a question about spot copies management by LIMMA. > I know that LIMMA needs all spots on the array are in the same number of copy ( e.g. each spot in double ). > In my research group It is just starting a project in wich we use Agilent microarrays (so high density microarrays) and on these arrays there is only a block of probes, positioned in a random fashion, in more than one spot for each probe. Moreover there is not the same number of copies for each probe in this block. Then we have not regularly spaced replicate spots on the same array. > Please, check the gal file by human Agilent microarrays sent as Email attachment, in which I highlighted in red some spots (but not all...) to better explain to you this situation. > Is LIMMA able to manage this situation? > That is, is LIMMA able to use this kind of random replicated spots to perform a quality control procedure, to fit the linear model and to produce a unique fold change value for this probe? > Can I use any kind of strategy to solve this problem? > Does It exists a free package that does this? > > Thank you very much for any information about this topic. > > Best Regards > > Erika Melissari >