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In most articles on this subject, a cut-off value is chosen for the various quality measures, and spots not satisfying these conditions are removed from further analysis. According to [1], one should be careful when doing this though, since sometimes what looks like a problem with the data, may come from natural causes, thus removing them may introduce bias, instead of removing it. Weighting spots, depending on their quality score, instead of removing them, could therefore be a better choice. This allows you to continue to use spots when doing e.g. normalisation. Another reason for introducing weights instead of cut-off values is that, according to [2], the values on the quality scores are very dependent on the methods used during the image analysis.
Bjørn Kåre Alsberg 2006-04-06