Hi Jim

Yes it has been tested on those array types, see
http://bioinformatics.picr.man.ac.uk/research/software/simpleaffy/testingmas5.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

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