AffyMAPSDetector: A Tool for Analyzing SNPs in GeneChip Expression Arrays
Author Information
Author(s): Kumari Sunita, Verma Lalit K, Weller Jennifer W
Primary Institution: Indiana University Purdue University Indianapolis
Hypothesis
The presence of allelic variants from SNPs may cause discrepancies in probe signal intensities on Affymetrix GeneChip™ arrays.
Conclusion
AffyMAPSDetector effectively characterizes SNP-containing probes, enhancing our understanding of their impact on gene expression measurements.
Supporting Evidence
- AffyMAPSDetector identified 7,286 probes with SNPs from the HG-U95Av2 GeneChip™.
- The tool showed that SNP-containing probes had distinct intensity distributions compared to non-SNP probes.
- Using SNP information improved the accuracy of gene expression measurements.
Takeaway
This study created a tool to help scientists understand how certain genetic variations can affect the results from gene tests, making it easier to analyze data.
Methodology
The study developed a Java-based software tool that identifies SNP-containing probes in Affymetrix expression arrays and analyzes their impact on gene expression data.
Potential Biases
Potential biases may arise from the misinterpretation of probe signals due to SNP presence.
Limitations
The tool's effectiveness may vary with updates to SNP databases and the complexity of probe designs.
Participant Demographics
The study analyzed data from 139 unique lung adenocarcinoma positive samples.
Digital Object Identifier (DOI)
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