These experiments used whole-genome arrays designed by Agilent Technologies. They were constructed of 60-mer oligonucleotides designed to match predicted genes in D. melanogaster genome release 3.0. In total, there are data for approx. 12,000 genes. A complete description of the platform and genes can be downloaded from the first author's homepage.
Two parental strains were used for experiments, Oregon-R and Russian 2b. The F1 hybrid offspring were also used, however, for Sebida we only include data for the parental strains. The cDNA was derived from week-old, whole males and females. In total, 7 replicate hybridizations were performed for each male- and female- derived cDNA, including biological and dye-swap replicates. In most cases, these hybridizations were not "head-to-head" male vs. female on the same array. Instead, the signal intensity for each probe was normalized relative to the intensity of all other spots in the same channel. The male/female ratios given in Sebida represent the ratio of the relative least squares mean intensities provided in the authors supplemental file .
P-values were calculated from the raw data using a Bayesian method (BAGEL) developed by Jeffrey Townsend. Because BAGEL requires male/female expression ratios, we paired the results of independent male and female hybridizations. When possible we used male and female data from the same array, otherwise they were paired randomly. BAGEL analysis was performed separately for the Oregon-R and Russian 2b strains, as well as for both strains combined.
In cases where there was more then one probe per gene, we used the average over all probes. Note that the ratios presented in Sebida are straight ratios and not ln or log2 transformations.