Hi Jim Yes it has been tested on those array types, see http://bioinformatics.picr.man.ac.uk/research/software/simpleaffy/test ingmas5.html Yes scaling factor is highly dependent on the target intensity used for scaling. The Affymetrix recommendations are that scale factors for ALL arrays within an experiment, or that will be analysed together, all fall within three-fold of each NOT that they are less than 3 Hope this helps Claire [[alternative HTML version deleted]]