First, we have provided a software tool for array analysis that should help you get through the initial stages of analysis. Currently we do not provide custom analysis services, so your best bet is to establish a scientific collaboration with members of the informatics group at Columbia. See Microarray Software Information for information on software we have used, and tools which are available at Columbia. See Microarray Software Information for information on software we have used, and tools which are available at Columbia. Because two-color arrays involve the use of two independent RNA samples that might vary slightly in concentration, and two separate labeling reactions which might have proceeded at different efficiencies, the overall brightness of the signal from one sample is often brighter than that from the other.
Normalization refers to the correction.
The correction factor is applied to each ratio. This method is based on the assumption that the average gene expression ratio on your array is 1. The advantage of this method is that you can do it on any array. This is the only method currently implemented in our analysis software. This procedure requires that your arrays include a number of control cDNAs which will not normally be present in your sample.