The analysis was performed with open source R software packages (http://www.r-project.org/ and http://www.BioConductor.org/). Gene expression was quantified with the array package using print tip group lowess normalization without background subtraction. The resulting measures of expression for each array are the log2 ratios (M values) and the average log2 intensities (A value) of Cy3 and Cy5 signals. Statistics of differential expression between the different groups of samples were calculated with a linear model fitted by the limma package.