Simple method to correct gene-specific dye bias from partial dye swap information of a DNA microarray experiment

In a cDNA microarray experinlent using Cy3 and Cy5 as labeling agents, particularly for the direct design, cDNAs from some Genes incorporate one dye more efficiently than the other, which is referred to as the gene-specific dye bias. Dye-swaps, in which two dyes are switched oil replicate arrays, are commonly used to control the gene-specific dye bias. We developed a simple procedure to extract the gene-specific dye bias information from a partial dye swap experiment. We detected gene-specific dye bias by identifying outliers in an X-Y plane, where the X axis represents the average log-ratio from two sets of dye swap pairs and the Y axis exhibits the average log ratio of four forward labeled arrays. We used this information for detecting differentially expressed genes, of which the additionally detected genes were validated by real-time RT-PCR.