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

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 expression profile showed a large variance across the different time points. Assessing the similarity in profile shape, it appears that, the more similar the underlying principles of the methods (model and input data), the more similar their results. Methods with a dye effect seemed more robust against array failure. The influence of a different normalization was not drastic and independent of the method used.Including a dye effect such as in the methods lmbr_dye, anovaFix and anovaMix compensates for residual dye related inconsistencies in the data and renders the results more robust against array failure. Including random effects requires more parameters to be estimated and is only advised when a design is used with a sufficient number of replicates. Because of this, we believe lmbr_dye, anovaFix and anovaMix are most appropriate for practical use.Microarray experiments have become an important tool for biological studies, allowing the quantification of thousands of mRNA levels simultaneously. They are being customarily applied in current molecular biology practice.In contrast to the Affymetrix based technology, for the two-channel microarray technology assays, mRNA extracted from two conditions is hybridised simultaneously on a given microarray. Which conditions to pair on the same array is a non trivial issue and relates to the choice of the "microarray design". The most intuitively interpretable and frequently used design is the "reference design" in which a single, fixed reference condition is chosen against which all conditions are compared. Alternatively, other designs have been proposed (e.g. a loop design). From a theoretical point of view, these alternative designs usually offer, at the same cost, more balanced measurements in the number of replicates per condition than a common referenc