qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data Article Swipe
Necla Koçhan
,
G. Yazgı Tütüncü
,
Gordon K. Smyth
,
Luke C. Gandolfo
,
Göknur Giner
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/751370
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/751370
Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine. We propose a new classification method based on a model where the data is marginally negative binomial but dependent, thereby incorporating the dependence known to be present between measurements from different genes. The method, called qtQDA, works by first performing a quantile transformation (qt) then applying Gaussian Quadratic Discriminant Analysis (QDA) using regularized covariance matrix estimates. We show that qtQDA has excellent performance when applied to real data sets and has advantages over some existing approaches. An R package implementing the method is also available.
Related Topics
Concepts
Linear discriminant analysis
Quadratic equation
Transformation (genetics)
Quadratic classifier
Mathematics
Negative binomial distribution
Covariance matrix
Quantile
Gaussian
Covariance
Artificial intelligence
Computer science
Data mining
Pattern recognition (psychology)
Algorithm
Statistics
Support vector machine
Gene
Biology
Poisson distribution
Physics
Biochemistry
Geometry
Quantum mechanics
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/751370
- https://www.biorxiv.org/content/biorxiv/early/2019/09/22/751370.full.pdf
- OA Status
- green
- Cited By
- 2
- References
- 29
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2971354641
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2971354641Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/751370Digital Object Identifier
- Title
-
qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq dataWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2019Year of publication
- Publication date
-
2019-08-31Full publication date if available
- Authors
-
Necla Koçhan, G. Yazgı Tütüncü, Gordon K. Smyth, Luke C. Gandolfo, Göknur GinerList of authors in order
- Landing page
-
https://doi.org/10.1101/751370Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2019/09/22/751370.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2019/09/22/751370.full.pdfDirect OA link when available
- Concepts
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Linear discriminant analysis, Quadratic equation, Transformation (genetics), Quadratic classifier, Mathematics, Negative binomial distribution, Covariance matrix, Quantile, Gaussian, Covariance, Artificial intelligence, Computer science, Data mining, Pattern recognition (psychology), Algorithm, Statistics, Support vector machine, Gene, Biology, Poisson distribution, Physics, Biochemistry, Geometry, Quantum mechanicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
2Total citation count in OpenAlex
- Citations by year (recent)
-
2021: 1, 2019: 1Per-year citation counts (last 5 years)
- References (count)
-
29Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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