CodeLink (GE Healthcare formerly Amersham Biosciences, Chandler, AZ) and GeneChip (Affymetrix, Santa Clara, CA) microarray platforms utilize oligonucleotide gene target probes of 30 and 25 bases, respectively.
The most significant disadvantages of microarrays include the high cost of a single experiment, the large number of probe designs based on sequences of low-specificity, as well as the lack of control over the pool of analyzed transcripts since most of the commonly used microarray platforms utilize only one set of probes designed by the manufacturer.
An important feature of the microarray platform utilized in our study is the coverage of non-coding Synechocystis genes.
Finally, although the microarray platform utilized in this study (the Illumina 27K Methylation Array) is reliable and has been previously used to identify quantitative changes in DNA methylation (51), it is relatively limited in the density of probe coverage, interrogating only a couple of CpG sites for the majority of genes with a bias to loci implicated in cancer.
Although cross-hybridization of AFAS probes with transcripts must be considered, our results reveal that our microarray platform utilizing the AFAS probes and the random priming method to prepare transcripts has the capacity to detect novel transcripts from the antisense strand.
Different microarray platforms employ different designs.
In addition, 65 samples from Illumina and Swegene microarray platforms were utilized as validation datasets.
Microarray platforms that utilize oligonucleotide DNA probes corresponding to predicted open reading frames (ORFs) have provided a reproducible approach to analyze changes in mRNA levels, allowing meaningful analyses of patterns of gene expression in a variety of cellular systems and model organisms [37].
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.
We found the much smaller difference of MM enrichment scores in colon cancer (0.34) and breast cancer (0.46), both of which had same pathological settings, although different microarray platform were utilized in breast cancer.
