Correcting positional correlations in Affymetrix® Genome Chips
Open accessAbstract
We report and model a previously undescribed systematic error causing spurious excess correlations that depend on the distance between probes on Affymetrix® microarrays. The phenomenon affects pairs of features with large chip separations, up to over 100 probes apart. The effect may have a significant impact on analysis of correlations in large collections of expression data, where the systematic experimental errors are repeated in many data sets. Examples of such studies include analysis of functions and interactions in groups of genes, as well as global properties of genomes. We find that the average correlations between probes on Affymetrix microarrays are larger for smaller chip distances, which points out to a previously undescribed positional artifact. The magnitude of the artifact depends on the design of the chip and we find it to be especially high for the yeast S98 microarray, where spurious excess correlations reach 0.1 at a distance of 50 probes. We have designed an algorithm to correct this bias and provide new data sets with the corrected expression values. This algorithm was successfully implemented to remove the positional artifact from the S98 chip data while preserving the integrity of the data.
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Positional effects due to technical variability manifest as distinct spatial patterns across rows, columns and edges in different plates.
“In contrast, positional effects due to technical variability manifest as distinct spatial patterns across the rows, columns and edges in different plates, a common challenge in multi-well-based assays30–33.”
From A statistical framework for high-content phenotypic profiling using cellular feature distributions (2022) · cites this paper as [33]
The Results (Evidence of positional artifact; page unavailable) describe a spatial, distance-dependent correlation pattern on Affymetrix chips that the authors propose arises from experimental systematic errors. The Discussion says the artifact varies across chip platforms. The paper does not establish row, column, or edge patterns in multi-well plates; it also attributes one prominent x-axis pattern to the arrangement of genes on the chip rather than technical variability. (LLM, conf=0.87)
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Self-citation
- Authors
- Homouz, D., Chen, G., & Kudlicki, A. S.
- Affiliations
- Khalifa University of Science and Technology (AE)
- BGI Group (China) (CN)
- The University of Texas Medical Branch at Galveston (US)
- Corresponding author
- Homouz, Dirar
- Venue
- Scientific Reports
- Published
- 2015-03-13
- Volume
- 5
- Issue
- 1
- Pages
- 9078-9078
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC4649851
- OpenAlex
- W2061579560
- Cited by
- 4
- References
- 32
- Citations by year
- 2022: 1 · 2019: 2 · 2017: 1
- FWCI
- 0.14
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- March of Dimes Foundation
- National Institutes of Health (UL1TR000071)
- National Center for Advancing Translational Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Affymetrix microarrays, systematic measurement errors
- MeSH terms
- Models, Theoretical, Yeasts, DNA Probes, Artifacts, Computational Biology, Oligonucleotide Array Sequence Analysis, Genomics, Databases, Nucleic Acid
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