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The 228 genes identified with COO differential expression from Stranger et al. samples (Illumina platform) were validated across platforms using an independent study of the same samples from the CEU and YRI populations on the Affymetrix GeneChip Human Genome U133 Array Set HG-U133A (15).
In order to validate robustness across platforms, the pathway over-representation analysis was repeated using the web-based toolkit WebGestalt (bioinfo.vanderbilt.edu/webgestalt/) and the online database resources KEGG (genome.jp/kegg/) and WikiPathways (wikipathways.org).org
In order to determine whether the disease signal could be validated using an alternative methodology, we applied the method of Cheadle et al [32] to validate across chip platforms.
Automate rigorous unit and regression tests to verify and validate the system across platforms.
However, in the neuronal dataset, alterations in gene expression between schizophrenia and control could not be validated across chip platforms (Table 7).
This observation has been validated across different platforms and across a spectrum of coverage (Supplementary Fig. S1).
In addition to well-known iNPH markers, Evans' index and recently validated DESH pattern [ 33] it offers the possibility to perform automatic volume estimates validated across MRI-platforms on older subjects [ 34].
Furthermore, the demonstration of IL-8 and SLC1A3 expression at the protein level in human osteosarcoma patient (TMA) samples validated the potential relevance of this comparative approach across platforms.
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