G-spots in Microarrays Affect Gene Expression Measurement
Author Information
Author(s): Graham JG Upton, William B Langdon, Andrew P Harrison
Primary Institution: University of Essex
Hypothesis
Do G-spot probes in Affymetrix microarrays lead to incorrect gene expression measurements?
Conclusion
G-spot probes should be excluded from gene expression calculations as they do not correlate well with other probes in their sets.
Supporting Evidence
- G-spot probes are poorly correlated with other probes in their sets.
- Over 40% of probesets in the HG-U133A GeneChip contain at least one G-spot probe.
- Correlation coefficients were calculated from 6685 HG-U133A CEL files.
Takeaway
Some probes in gene tests can give wrong results because they behave differently than expected, so we should ignore them.
Methodology
The study analyzed correlation coefficients between probe pairs from thousands of microarray datasets to identify poorly performing probes.
Potential Biases
Potential bias due to the exclusion of certain probes may affect overall gene expression results.
Limitations
The study focused only on Affymetrix HG-U133A arrays and may not apply to other microarray platforms.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website