Extensive efforts to characterize the reproducibility of microarray methodologies and platforms have been carried out previously [21], [22], showing that careful attention to methods can yield predictable reproducibility.
Using this approach not only can mRNA levels be validated, but also differences in microarray methodology, normalization and data processing methods.
These observations are consistent with previous reports of gene expression profiling using microarray methodology [ 36], and provide validation of the RT-PCR assays.
The lack of agreement between these studies is probably due to differences in the animal models (parenteral vs. enteral iron loading; mouse strains) and in the microarray methodology.
In addition, the large number of differentially expressed genes we observed may reflect the high sensitivity and repeatability of the microarray methodology employed, where small technical variances generated high power for the detection of differential expression.
It has been demonstrated that classification gene sets are profoundly influenced by the microarray methodology, such as the microarray technique, microarray platform, and preprocessing methods [ 4- 8].
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].
Microarray methodology simultaneously measures the expression levels of a large number of genes, and the expression levels of several genes are frequently analyzed collectively.
We use high-resolution microarray methodology [ 37] to comparatively study gene expression for ~42,000 genes in diploid and allotetraploid cotton species at an early stage of fiber development.
For the first time the microarray methodology has been applied for the simultaneous identification of different mixed population of spoilage yeast and bacteria directly isolated from wine, thus indicating the practicability of oligonucleotide microarrays as a contamination control in wine industry.
