Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes
Open accessAbstract
Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalization fail. Specifically, this can occur when specialized boutique arrays are constructed that contain a subset of genes selected to test particular biological functions.
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This weighting ability has been exploited for normalizing assays when the proportion of differentially expressed genes may be high, for example boutique arrays, miRNA arrays, PCR arrays, protein arrays or protein mass spectrometry.
“The latter ability has been exploited for normalizing assays when the proportion of differentially expressed genes may be high, for example boutique arrays (39), miRNA arrays (40), PCR arrays, protein arrays or protein mass spectrometry.”
From limma powers differential expression analyses for RNA-sequencing and microarray studies (2015) · cites this paper as [39]
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References 23 · Cited by 69
- Authors
- Oshlack, A., Emslie, D., Corcoran, L. M., & Smyth, G. K.
- Affiliations
- Walter and Eliza Hall Institute of Medical Research (AU)
- Corresponding author
- Oshlack, Alicia
- Venue
- Genome biology
- Published
- 2007-01-04
- Volume
- 8
- Issue
- 1
- Pages
- R2-R2
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC1839120
- OpenAlex
- W2140774750
- Cited by
- 69
- References
- 23
- Citations by year
- 2026: 2 · 2024: 1 · 2023: 1 · 2022: 2 · 2020: 2 · 2019: 2 · 2018: 1 · 2017: 2 · 2016: 2 · 2015: 4 · 2014: 5 · 2013: 6 · 2012: 4
- FWCI
- 3.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- Funders
- National Health and Medical Research Council (406657)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- microarray normalization, two-color microarrays, lowess normalization, systematic variation, gene expression bias
- MeSH terms
- Animals, B-Lymphocytes, Color, DNA Probes, Up-Regulation, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Mice
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