Verifying Affymetrix Probe Sequences for Accuracy
Author Information
Author(s): Alberts Rudi, Terpstra Peter, Hardonk Menno, Bystrykh Leonid V, de Haan Gerald, Breitling Rainer, Nap Jan-Peter, Jansen Ritsert C
Primary Institution: University of Groningen
Hypothesis
How accurate are the probe sequences of Affymetrix genome arrays for studies in mouse, human, and rat?
Conclusion
The accuracy of Affymetrix probe sequences is higher than previously reported, especially on newer arrays, and using refined probe set definitions improves the detection of differentially expressed genes.
Supporting Evidence
- 85% of the probes were verified for the U74 array.
- 95% of the probes were verified for the 430 array.
- Refined probe definitions significantly improved the detection of differentially expressed genes.
Takeaway
This study checks if the probes used in certain gene tests are correct. It found that most of them are accurate, which helps scientists get better results.
Methodology
An extensive verification protocol was developed using multiple databases to assess the accuracy of probe sequences in Affymetrix arrays.
Potential Biases
Potential bias due to reliance on specific databases for verification.
Limitations
The study primarily focused on specific mouse strains and may not account for variations in other strains.
Statistical Information
P-Value
p<1E-10
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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