More recently, a low-density microarray utilizing the NanoChip400 system (Nanogen Inc), which employs one probe for the conserved M gene and 97 probes for the cleavage site region of HA gene, was described to be a useful diagnostic tool for H5N1 virus [ 29, 30].
The microarray utilized was the commercially available Affymetrix GeneChip® Cotton Genome Array (Affymetrix Inc., Santa Clara, CA), that represents 21,854 transcripts gathered from four species of cotton (G. arboreum, G. barbadense, G. hirsutum, and G. raimondii) and a variety of tissue types including fibers at the initiation, elongation, and SCW biosynthesis stages of development.
Their results showed that the microarray utilized in this study was able to distinguish between the mismatched sequences, but was unable to distinguish between the highly similar sequences [13].
Our microarray data utilized the Affymetrix ATH1 chip and are from hybridizations described in detail in [ 31].
For comparison based on the biological function for the differentially expressed genes from RNA-seq and microarray, we utilized the ClueGO to integrate the Gene Ontology (GO) [ 65] terms and KEGG [ 66] pathway terms and create a functionally organised GO/KEGG network.
To obtain an estimate of the number of expressed genes measured by the microarrays, we utilized the arrays' unique feature that they included probes for Prochlorococcus MIT9313 and several phages besides probes for Prochlorococcus MED4.
Previous comparisons involving microarrays have utilized the signal intensities [ 4, 12- 19].
RNA cardiac samples from six individual fish from each dietary group and sampling point were used in the microarray analysis, utilizing the Atlantic salmon SIQ2 microarray [ 18] in a one-color setup, resulting in a total of 24 arrays.
To assess signal repeatability and reproducibility of each microarray platform, we utilized the methods that the MAQC Project used [6], such as calculating the Spearman's correlation coefficient (Rs), and the coefficient of variation (CV) of the signal or Cy3/Cy5 values for one or two color method, respectively.
Once the various expressed genes have been collected in the database, we could design microarrays utilizing these genes while omitting rRNA genes.
