In addition, published comparison of different microarray platforms suggests strong platform-specific effects (Detours et al, 2003), raising the possibility that our results relying on Micromax arrays may not be reproducible on other platforms.
Xu et al. [ 26] compared transcriptome profiles that were generated by Illumina RNA-Seq and Affymetrix microarray platforms, and their results suggested that RNA-Seq is more advantageous for detecting genes with low-level expression compared with microarrays.
All GO categories associated with more than five genes are shown in Additional file 2. The combined use of multiple microarray platforms has recently been suggested as an alternative that is complementary to qRT-PCR for validation of gene expression profiles [ 31- 33].
As this observation holds for multiple mouse and human TFs from different microarray platforms (GPL1261 and GPL96), our results suggest that biological variability in the publicly available Affymetrix microarray data is stronger than the laboratory or batch effects.
The results of this study suggest that currently available microarray platforms are complementary (i.e., not all CNVs are captured by one platform/array design) and that the number and type of CNVs detected varies depending on microarray probe distribution, sample labeling and hybridization chemistries, and CNV detection algorithms used.
This platform comparison analysis suggests that use of multiple microarray platforms provides complementary data as every microarray platform detects a unique set of novel CNVs.
These studies suggest that one of the main reasons for inconsistencies between different microarray platforms is the differences in the gene regions chosen to be printed for each platform.
This strongly suggests that predictive models could be successfully developed using different microarray platforms as long as classifiers with the best performance could be constructed for each platform.
Previous reports have explored gene co-expression networks derived from heterogeneous microarray platforms [ 14, 34] and confirm that observing a conserved gene co-expression suggests a biological relevance [ 9, 35].
This has previously been suggested as a reason for discrepancy between cDNA- and oligonucleotide-based microarray platforms in expression ratios [ 38].
