microarrays measure only the relative quantities of transcripts. Specifically, this technology suffers from fluorescence background and cross-hybridization problems that might lead to underestimating low-abundance transcripts or the expression levels of infrequently expressed genes. Second, the technique measures the activity of previously identified genes—array probes represent a predefined set of well-annotated genes. Correspondingly, this leads to underestimating new transcripts and splicing forms of a transcript, which are produced by ~95% of the multiexonic genes in the human genome (Pan, Shai, Lee, Frey, & Blencowe, 2008). Third, there is a lack of universal standards among the different platforms (e.g., differences in numbers of probes, probe designs and concentrations, the usage of fluorescent dyes to characterize different stabilities, and quantum efficiency in response to light) that result in some inconsistencies between the data obtained via different platforms. Even within the same array type there are problems with the low reproducibility of results among different experiments and different labs due to differences in RNA target preparation for hybridization and data analytic methods (Irizarry, et al., 2005; Kawasaki, 2006; Pedotti, et al., 2008).
