7.7 years ago by
Maastricht, The Netherlands
For Affy, at least traditional Affy, Wills answer makes most sense. But you can in fact have multiple probes for the same gene on other arrays as well. If you just want a quick solution taking the median is often the best solution. If you have more than two that will make sure you get rid of any real outliers, that can originate from problems like David mentioned in his comment. If you are really interested in one specific gene simply look at the raw data and even the raw image and try to make sense of it. Sometimes one of differing spots is simple in a bad area. Sometimes one of sequences shows cross hybridization problems when you BLAST them all. Sometimes there really is nothing you can see and the sequences turn out to (almost completely overlap), then you are back with the default solution: just take the median.