Hello, I'm trying to analyze a set of Combimatrix arrays with LIMMA and have a couple of questions. I haven't found anything on this list about Combimatrix arrays, so I might just start by noting what I'm doing with them, which may or may not be sensible. They are single color arrays. It's not possible to estimate a spotwise background intensity for these arrays, so I assume it is uniform over the whole array. I'm using "normexp" for background correction, then quantile normalization. The arrays have some duplicated spots (sometimes 3x, sometimes 4x), haphazardly arranged. I'm currently just averaging these duplicates. How important is the business with ndups and duplicateCorrelation to the final result, am I losing much by just averaging? My second question is is it possible to obtain a "moderated" standard error? If I do an MA plot, it's not clear why the top probes were chosen, as they sometimes have smaller M than other probes. I'd like to show error bars to give an indication of our confidence in each spot. I imagine it's just a matter of multiplying or dividing a couple of the vectors in the fitted model object, but I'm afraid that if I try to guess which I will inadvertantly commit a small crime against statistical sanity. -- Paul Harrison Victorian Bioinformatics Consortium / Monash University pfh at logarithmic.net jabber pfh at njhurst.com icq 298231643 http://www.logarithmic.net/pfh/