Because of the limited availability of expressed sequence tags (EST) and cDNA sequences at earlier stages, limited probes were printed for microarray analysis; thus, limited genes were analyzed (Kawasaki et al. 2001).
For one, the scarce number of samples included in the microarray analysis may limit the validity of the array results.
However, microarray analysis is limited in detecting RNA transcript isoforms, whereas deep sequencing reveals the rich abundance of isoforms at each gene locus [ 7, 21].
Despite its throughput and global profiling ability, microarray analysis was limited by its requirement for high amounts of starting material to produce robust results.
The microarray analysis is limited by the set of genes on the arrays, whereas polymerase chain reaction differential display (PCR-DD) randomly samples the transcriptome.
A second microarray cohort analysis limited to non-diabetics from the multi-center PREDICT study (198 patients; 99 case: control pairs matched for age and sex) evaluated gene expression, clinical, and cell population predictors of CAD and yielded 5,935 CAD genes (p < 0.05) with an intersection of 655 genes with the CATHGEN results.
Genetic markers for thyroid cancers identified by microarray analysis have offered limited predictive accuracy so far because of the few classes of thyroid lesions usually taken into account.
However, as the initial study of the salm mutant IFMs was performed by microarray analysis which provided limited coverage of the various gene isoforms 7, it remained unclear to what extent alternative splicing contributes to the muscle fiber-type switch.
Microarray analysis is much less limited by the presence of highly abundant transcripts, because each mRNA binds independently to its complementary sequence feature on a microarray.
Apart from the technical challenges of microarray analysis this study is limited in resolution ability by the low sampling rate of circadian time series.
