Statistical considerations in the assessment of cDNA microarray data obtained using amplification

Data acquisition is the critical first step in microarray studies to profile gene expression. Successful data acquisition depends on obtaining consistent signals above the level of the background noise on the microarray. Many factors influence the quality and quantity of the fluorescent signals obtained from microarray experiments, including the strength of the fluorescent dyes, the sensitivity of the scanners that detect the signals, and the amount of labeled cDNA targets applied to the microarray. In order to increase signal intensity, substantial efforts have been made to develop stronger dyes and to improve the sensitivity of the scanners. Both laser and CCD based scanners have been developed, but most commercially available scanners have similar performances (Ramdas et al., 2001). Technological improvements in dyes and scanners, by themselves, have provided incomplete solutions to the problem of generating strong, reproducible signals from microarray experiments using small amounts of starting materials.