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Interestingly, in all cases meaningful partitioning results were obtained using inflation parameter set to 2. We next applied DBF-MCL algorithm to all experiments performed on human, mouse and rat Affymetrix microarrays and available in the GEO database (33 platforms, Supplementary Table S1 and S2).
The methods that are used in glycan microarrays and available databases are discussed below.
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The data are from the work of Gibson et al. [ 1] with Agilent 60-mer oligonucleotide microarrays, and are available online [ 32].
Based on statistical analysis of microarray data and available gene information, including previous reports, 32 genes were chosen for qPCR confirmation and validation (Table 3).
HapMap CEU and YRI datasets processed on four different Illumina microarray chips and available in the NCBI GEO database [ 25] were analyzed by triPOD (NC ≤ 5%).
Both data sets are from Affymetrix high-density oligonucleotide microarrays and are publicly available [16].
> The continuous technological improvements of DNA microarrays and the commercially available platforms provide the basis for wide application of the technology.
The data used in this study were generated on Affymetrix U133A oligonucleotide microarrays and are publicly available [ 7, 8, 16- 18].
We have made all microarray data MIAME compliant and available through the public databases of NCBI-GEO (accession numbers: GSM472993, GSM472992, GSM472991, GSM472990, GSM472989, GSM472988).
However, these studies were conducted before microarrays became available and did not begin to approach genome-wide scans.
We modified DNA library preparation for the Illumina Genome Analyzer to allow the small amounts of ChIP-enriched DNA to be simultaneously used on both commercially available microarrays and Illumina sequencers (Figure 1A).
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