Given that different microarray platforms have multiple probes for a single gene, the cross-referencing of such platforms generates numerous combinations of expression values for a given gene (32160 in this study).
In two independent groups of adults with epilepsy and co-morbidities, we identified copy number variants judged to be of pathogenic significance in 13.5% (7/52) and 20% (5/25) respectively, noting that different criteria and microarray platforms were used, giving an overall yield of 15.6%, in keeping with the literature [1].
Microarray platforms, in particular, have given enormous momentum to the study of brain gene regulation in the contexts of sensory/motor processing, learning, the formation of memories, aging, and the onset of diseases [1] [6].
To identify deregulated miRNAs in male breast cancers, the miRNA expression profiles were determined for five male gynecomastia samples, 23 male breast cancer samples and 10 female breast cancer samples using a custom microarray platform proven to give robust results, as validated by several studies [ 3, 4, 10, 12].
There are two major microarray platforms that have been widely used: cDNA microarrays and oligonucleotide microarrays.
The top 50 discriminator genes over all four microarray platforms are shown in Figure 3 (complete list is given as Additional file 9).
The cost factor is especially important, given the fairly high cost of microarray platforms and the subsequent burden the resulting data place on experts in an organization in terms of time and electronic data management.
Finally the TBMap plugin that can be used to visualize a summary of transcriptional regulation events observed in a given microarray platform will be presented in the last paragraph of the results section.
Data normalization: a global normalization was performed across all data from a given microarray platform (see Methods section).
The background gene set could be all of the probes for a given microarray platform, while the resultant gene set would include only the differentially expressed genes.
