Effects of Normalization Methods on Gene Expression Linkage Results
Author Information
Author(s): Mariza de Andrade, Elizabeth J Atkinson, Brooke L Fridley, Ellen L Goode, Shannon McDonnell, Wen Liu-Mares, Kari G Rabe, Zhifu Sun, Susan L Slager
Primary Institution: Mayo Clinic College of Medicine
Hypothesis
How do different normalization methods for gene expression data affect linkage results?
Conclusion
Normalization methods significantly influence linkage results, with dChip normalization yielding higher LOD scores than Affy normalization.
Supporting Evidence
- The dChip normalization method yielded LOD scores > 3.0 30% more frequently than the Affy normalization.
- There was a high correlation (r = 0.97) between the two normalization methods for the selected phenotypes.
- Normalization methods play an important role in the linkage results.
Takeaway
This study looked at how two ways of processing gene data can change the results we get when trying to find genetic links. One method gave higher scores than the other.
Methodology
The study used two normalization methods (Affy and dChip) on 3554 expression phenotypes and performed a genome-wide linkage scan using 2272 SNPs.
Potential Biases
Potential bias due to the choice of normalization method affecting linkage results.
Limitations
The study could not compare all findings with previous research due to differences in selected phenotypes.
Participant Demographics
196 participants from 14 three-generation pedigrees.
Statistical Information
P-Value
<10-8
Statistical Significance
p<0.0001
Want to read the original?
Access the complete publication on the publisher's website