The expression values of target genes (probe sets) are derived from the signal intensities of those 11 PM probes using the signal condensing methodology such as the Microarray Suite (MAS) 5.0 (http://www.affymetrix.com) or the Robust Multi-array Average algorithm (RMA) [ 35].
Advances in methodology such as high-resolution microarrays and sequencing may have removed the influence of the bias, suggesting that literature bias favoring well-studied genes may correct itself as more genes become better characterized.
Thus, differential expression detected by microarray analysis is highly predictive of expression levels measured with an independent methodology such as Q-PCR (80% confirmation).
Recently next generation sequencing technology in combination with microarray methodology [ 16] has been demonstrated to be a fast and reliable tool for analysis of large genes such as NEB[ 15].
The resolution of this microarray methodology is ∼15% in exon inclusion differences [15].
Technical replication and normalization of data are well-validated approaches to deal with variability in other genomic methodologies, such as microarray transcript expression profiling[20].
To characterize the small RNA transcriptome, the new 'deep-sequencing' technologies, such as Roche 454 and Illumina Solexa, have been employed which have significant advantages over previous hybridization-based methodologies, such as microarray and PCR-based assays [6], [7].
In conclusion, MgC-GEP adopts covnentional RT-PCR, restriction enzyme digestion, concatemer ligation, bacterial transformation and DNA sequencing to assess mRNA profiles without using high-throughput expensive methodologies such as microarray hybridization or deep sequencing.
These limitations are disappearing with the advent of methodologies such as microarrays that facilitate rapid characterization of global gene expression at the level of individual cells and tissues.
Through the advent of global gene expression profiling methodologies such as microarrays, it has become possible to identify the consequences of these remarkably conserved chromosomal aneuploidies on the cancer transcriptome.
