Evaluation of time profile reconstruction from complex two-color microarray designs

Background: As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (more replicates of the conditions of interest for the same number of arrays). However, the interpretation of the measurements is less straightforward and a reconstruction method is needed to convert the observed ratios into the genuine profile of interest (e.g. a time profile). The potential advantages of using these alternative designs thus largely depend on the success of the profile reconstruction. Therefore, we compared to what extent different linear models agree with each other in reconstructing expression ratios and corresponding time profiles from a complex design. Results: On average the correlation between the estimated ratios was high, and all methods agreed with each other in predicting the same profile, especially for genes of which the expressi...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Ana C. Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal, Nicolas Pollet
• Keywords: BMCBI 2008, Design, Dye Effect, Profile