These experiments used genome tiling arrays of 36-mer oligonucleotide probes. In total, there were 179,972 unique probes. Of these, 61,371 exon probes assayed 52,888 exons from 13,197 predicted genes. In addition there were 87,814 nonexon probes designed to intronic and intergenic regions, and 30,787 splice junction probes. Details on the arrays and resulting data are available from Kevin White's web site. Only results from the exon probes with significant expression above background are included in Sebida.
Expression was assayed at several different developmental stages. Only hybridizations of adult males and adult females were included in Sebida. In total, 4 replicate hybridizations were performed for each sex, including biological and dye-swap replicates. In some cases, these hybridizations were not "head-to-head" male vs. female on the same array. For this reason, 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 average relative male and female intensities.
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.