Fig. 3b shows a comparison of the fold-changes measured using transcriptome sequencing of the A and B samples with the TaqMan results for 217 RefSeq genes that were detected at sufficient levels to be called "present" in both the A and B samples by TaqMan and by all the major commercial microarray platforms (ABI, Affymetrix, Agilent, GE, and Illumina)[ 1, 2].
The microarray data from external datasets were generated by using one of the three major commercial microarray platforms: Affymetrix GeneChip, Agilent oligonucleotide microarray and Illumina BeadChip.
The US Food and Drug Administration (FDA -led community-wide Microarray Quality Control (MAQC) study generates a large amount oFDA -ledrray data with implementation of ERCs across several commercial microarray platforMicroarray
This approach can be used with other commercial microarray platforms (Nimblegen, Affymetrix, or self-print microarrays).
Purified, labeled NRO cRNA can be then hybridized to most commercial microarray platforms (Illumina, Affymetrix, and Agilent were successfully tested).
They concluded that matching probe-sets within the same exons and using similar experimental protocols can lead to more reproducible results when performed on major commercial microarray platforms.
Other commercial microarray platforms (e.g. Nimblegen and Affymetrix) with higher oligonucleotide densities may have less sensitivity to signal fragmentation via probe loss.
Our results established that it is possible to successfully apply multiple-class prediction models across different commercial microarray platforms, offering a number of important benefits such as accelerating the possible translation of biomarkers identified with microarrays to clinically-validated assays.
To further establish the applicability of ANRO on different commercial microarray platforms, we calculated statistically significant regulated gene expression determined from a parallel series of experiments using both the Affymetrix exon array and Illumina BeadArrays.
Commercial microarray platforms perform better than the home-spotted mainly due to their higher reproducibility.
