TAESUNG PARK
Department of Statistics, Seoul National University, Seoul, Korea
KIWOONG KIM
Department of Statistics, Seoul National University, Seoul, Korea
SUNG-GON YI
Department of Statistics, Seoul National University, Seoul, Korea
JIN HYUK KIM
Department of Physiology, Hanyang University College of Medicine, Seoul, Korea
YONG-SUNG LEE
Department of Biochemistry, Hanyang University College of Medicine, Seoul, Korea
SEUNGYEOUN LEE
Department of Applied Mathematics, Sejong University, Seoul, Korea

Received 8 October 2006
Revised 2 April 2007
Accepted 11 April 2007

In two-channel microarray experiments, the image analysis extracts red and green fluorescence intensities. The ratio of the two fluorescence intensities represents the relative abundance of the corresponding DNA sequence. The subsequent analysis is performed by taking a log-transformation of this ratio. Therefore, the statistical analyses depend on accuracy of the ratios calculated from the image analysis. However, not many studies have been proposed for developing more reliable ratio statistics. In this paper, we consider a new type of log-transformed ratio statistic. We compare the new ratio statistic with the conventional ratio statistic commonly used in two-channel microarray experiments. First, under the specific log-normal distributional assumption, we compare analytically the new statistics with the conventional ratio statistic. Second, we compare those ratio statistics using a two-channel microarray data obtained by hybridizing a mixture of mouse RNA and yeast in vitro transcript (IVT). Both comparisons show that the proposed ratio statistic performs better than the conventional one.

Log-normal distribution; mean square errors; ratio statistic