What is the difference between scaling and normalization when I scale or normalize my data to all genes on the array?
When scaling the data, you designate an arbitrary target signal and the Microarray Suite software scales the average intensity of all genes on each array, within a data set, to the target signal you specified. This process enables you to compare multiple arrays within a data set. We advise that you use the same target signal across all arrays being compared. Scaling can be performed independently of the comparison analysis.
On the other hand, normalization can only be done when doing the comparison analysis in the Microarray Suite. In this case, the software compares an experimental array with a baseline array, and normalizes the average intensity of the experimental array to the average intensity of the baseline array during normalization. The normalization factor for a particular array changes when you change the comparison baseline array.