Tech Notes

Q. Do I need to normalize my scaled Affymetrix data in GeneSpring?

A. If your Affymetrix data is already scaled to a target intensity, it is not necessary to apply a "Per Chip" normalization step. Because GeneSpring automatically applies a per chip normalization to all imported Affymetrix data by default, you must specifically delete this step before proceeding. However, applying a "Per Chip: normalize to a median or percentile" or global normalization to prescaled data does not usually affect the resulting normalized values significantly.

NOTE: you should still apply a "Per Gene" normalization step to all Affymetrix data. For more information on what normalization to apply to your data, follow the guidelines given in our manual.