Peer Review #2 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.1)" Article Swipe
Necla Koçhan
,
G. Yazgı Tütüncü
,
Gordon K. Smyth
,
Luke C. Gandolfo
,
Göknur Giner
,
Necla Koc ̧han
,
G Özde
,
Y Üt Ünc
,
Göknur Giner
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.7287/peerj.8260v0.1/reviews/2
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.7287/peerj.8260v0.1/reviews/2
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 on https://github.com/goknurginer/qtQDA.
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- Type
- peer-review
- Language
- en
- Landing Page
- https://doi.org/10.7287/peerj.8260v0.1/reviews/2
- OA Status
- gold
- References
- 35
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4244260507
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Raw OpenAlex JSON
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https://openalex.org/W4244260507Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.7287/peerj.8260v0.1/reviews/2Digital Object Identifier
- Title
-
Peer Review #2 of "qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data (v0.1)"Work title
- Type
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peer-reviewOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2019Year of publication
- Publication date
-
2019-12-18Full publication date if available
- Authors
-
Necla Koçhan, G. Yazgı Tütüncü, Gordon K. Smyth, Luke C. Gandolfo, Göknur Giner, Necla Koc ̧han, G Özde, Y Üt Ünc, Göknur GinerList of authors in order
- Landing page
-
https://doi.org/10.7287/peerj.8260v0.1/reviews/2Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.7287/peerj.8260v0.1/reviews/2Direct OA link when available
- Concepts
-
Quantile, RNA-Seq, Quadratic equation, Linear discriminant analysis, Computer science, Statistics, Mathematics, Computational biology, Biology, Genetics, Transcriptome, Gene, Geometry, Gene expressionTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
0Total citation count in OpenAlex
- References (count)
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35Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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