Hi, we have just bought in a few microarray slides and they have each gene characterised by only a single spot. This is not really desirable as I would like to see (ideally) a triplicate or at least a duplicate of spots distributed for each gene to allow some kind of quality check (variability) as well as use some of the more advanced analysis tools on them. Can anyone point me to any published papers or working papers on slide design that cover these points: * single/duplicate/triplicate/many spots * advantages of replicate slides and dye swaps * comparison of side-by-side and distributed spot patterns (i.e., are distributed a la affy spot patterns any better than localised spots: spatial effects, artifacts and variability across the slide are some of the concerns I can think of) * Controls (scorecard and the like, housekeeping gene's, lighthouse spots, blanks, buffer spots etc) - this is a huge topic and there are a few papers out there on this, but if someone wants to comment ... Searches turn up a lot of empirical data and a few gems, but I would like to find more references to support an "ideal slide design for data analysis", to counter the idea that slide real-estate is expensive, so we must therefore crowd as much on a slide as possible so we can cover the largest number of gene's possible! Your thoughts please ... BillK -- William Kenworthy BioInformatics Officer Centre for BioInformatics and Biological Computing WA State Lotteries Microarray Facility W.Kenworthy@murdoch.edu.au +61 (0)8 9360 2790