Salvaging Affymetrix probes after probe-level re-annotation
2008
Salvaging Affymetrix Probes with CDF-Merger
publication
Evidence: moderate
Author Information
Author(s): Wim C de Leeuw, Han Rauwerda, Martijs J Jonker, Timo M Breit
Primary Institution: University of Amsterdam
Hypothesis
Can we restore lost Affymetrix probes after re-annotation to improve data quality?
Conclusion
The CDF-Merger algorithm successfully salvaged up to 94% of lost Affymetrix probes.
Supporting Evidence
- The CDF-Merger restored probe content up to 94%.
- Biologists can choose which subset of probe-sets to use in their analyses.
- The algorithm allows for easy implementation in R environments.
Takeaway
This study created a tool to help scientists keep more data from their experiments, even when some information is lost during updates.
Methodology
An algorithm called CDF-Merger was developed to merge and restore probe sets from Affymetrix GeneChips.
Limitations
The hybrid approach may dilute the quality of data from original re-annotation procedures.
Digital Object Identifier (DOI)
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