Because sex-bias classifications (and their statistical significance) vary among the published datasets, we performed a meta-analysis to classify sex-biased genes in D. melanogaster. This was done using the following datasets:

Innocenti et al. (2010)
Wyman et al. (2010)
Ayroles et al. (2009)
McIntyre et al. (2006) [Ore-R]
McIntyre et al. (2006) [2b]
Gibson et al. (2004) [Ore-R]
Gibson et al. (2004) [2b]
Parisi et al. (2003) [testes/ovaries]
Parisi et al. (2004) [whole fly]
Ranz et al. (2003)
male05/female05 (modEncode 2011)[male05/female05]
testes/ovaries (Gan et al. 2010)[testes/ovaries]

Since the Ayroles et al. (2009) and Innocenti et al. (2010) datasets had very high replication, they were given a weighting of 2 in the meta-analysis. All other datasets were given a weighting of 1.
The male/female (M/F) expression ratios from each of the above experiments were used as input for BAGEL (Townsend and Hartl 2002) to infer relative expression levels in males and females, as well as their 95% confidence intervals and the probability (P-value) of differential expression between the sexes. A maximum ratio of 32 was used; ratios above this were set to 32. The false discovery rate (FDR) associated with the P-values was determined be re-running the BAGEL analysis on random permutations of the input data. An FDR cut-off of 20% was used to classify sex-bias in the Sebida web entries, but other definitions can easily be applied to the downloadable dataset (see Download page). Genes with FDR>20% were classified as unbiased. A small proportion of genes that were not investigated in enough of the above datasets (a minimum of 3 is required) remain unclassified. Many of these are cases in which the annotation has changed among releases of the D. melanogaster genome sequence. The number of genes in each category for the different FDR cutoffs is shown below. Also shown is the number of genes in each category using a 2-fold cutoff (e.g., genes with a male/female expression ratio >2 are classified as male-biased, genes with a male/female expression ratio <0.5 are classified as female-biased).
The 2-fold cutoff is more conservative for classifying sex-biased genes. Almost all of the genes showing a 2-fold or greater difference in expression between the sexes are also highly significant in the statistical analysis. The following table shows the number of genes with a 2-fold difference between the sexes that fall into the different FDR categories.
FDR
2-fold Classification <1% 1-5% 5-10% 10-20% >20%
Male (2033 genes) 1871 100 28 21 13
Female (2028 genes) 1956 45 14 7 6