Custom Spotted Array Data Analysis

The Tif image created by the scanner is processed by imaging software, such as Imagene and ProScanArray Express. These applications are capable of spot-finding, background intensity determination, and signal intensity generation. The output is a tab-delimited text file, which has each spot’s intensity.

The process of analyzing the text file output is the most non-standardized aspect of custom chip data analysis. The first step is normalization. There are conflicting arguments in the literature as to what should be normalized for, i.e. channel, print tip, hybridization, etc., in addition to which algorithm should be used to normalize. Next, the investigator can perform basic statistics using the normalized values. The DNA array core has a full time statistician to assist with data analysis.