This has led to the suggestion that disagreements between microarray platforms may be due to cross-hybridization of the probes on the arrays with other targets [ 8].
A direct comparison of the results from the two microarray platforms is problematic due to the considerably greater number of gene models represented on the Nimblegen microarray used for the Pt-TC experiment (54,794 compared to 15,789).
Furthermore, the microarray platform has limitations due to cross-hybridization and relatively lower dynamic range.
Due to background, microarray platforms often cannot reliably measure expression in the low-intensity range.
Furthermore, different and improved microarray platforms have been used over time, due to the increased availability of improved microarray tools tailored to the genome sequence of most livestock species.
In this study we have excluded discrepancies due to different microarray platforms and our results argue against recent criticism that gene expression profiling may not be robust enough to be useful for clinical application [ 44, 45].
That there was not more correlation may be due to incomplete microarray platforms, but more importantly is likely to reflect the bias present in the published RUNX1 target genes that were identified because of their primary role in hematopoiesis and these may not represent the most common RUNX1 target genes.
Due to the different microarray platforms (Affymetrix, Agilent Technologies), experimental protocols and data processing for normalization used by authors, we choose to use gene expression raw data individually.
However, it is worthwhile noting that integrating microarray datasets from different studies is not so simple due to the different microarray platforms across different datasets, different experimental protocols, and different preprocessing methods.
The reason for this difference in the two data sets is likely due to the difference in microarray platforms used in these studies.
