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Robust gene set analysis and robust gene expression
Descriptive
TitleInfo
Title
Robust gene set analysis and robust gene expression
Name
(type = personal)
NamePart
(type = family)
Tang
NamePart
(type = given)
Ning
DisplayForm
Ning Tang
Role
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author
Name
(type = personal)
NamePart
(type = family)
Cabrera
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Javier
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Javier Cabrera
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Advisory Committee
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chair
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STRAWDERMAN
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WILLIAM E
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WILLIAM E STRAWDERMAN
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Advisory Committee
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internal member
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(type = family)
Dicker
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(type = given)
Lee
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Lee Dicker
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Advisory Committee
Role
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internal member
Name
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NamePart
(type = family)
Cheng
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(type = given)
Jerry
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Jerry Cheng
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Advisory Committee
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outside member
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Rutgers University
Role
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degree grantor
Name
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NamePart
Graduate School - New Brunswick
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school
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Text
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theses
OriginInfo
DateCreated
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2014
DateOther
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(type = degree)
2014-05
Place
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xx
Language
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(authority = ISO639-2b);
(type = code)
eng
Abstract
(type = abstract)
This paper explores various methods of statistical analysis of DNA microarray data. First, we review the RMA method which produces estimates of gene expression from a microarray data and propose a new version of RMA that is not only resistant to outliers but also has high efficiency. To construct our new RMA estimator we rely upon M-estimator of location, including Tukey’s biweight and Huber’s M-estimator. We compare the performance of our robust version of RMA with median, the currently used one in the RMA method, as well as mean, which is a non-robust estimator of location. Second, we review the Gene Set Enrichment Analysis (GSEA) methodology. Currently, the GSEA method is performed at gene-level. This requires DNA microarray data be transformed from the raw probe-level data to the gene-level data. This process cannot avoid losing subtle but crucial information contained in the probe-level data. Inspired by the GSEA method, we extend its idea to the probe-level data. Finally, we develop a family of enrichment method - Enrichment Analysis using M-estimator (EAME), which, as implied by its name, uses robust M-estimator and take advantage of the idea of gene set enrichment. At the end of this paper, we use the R language as a tool to show some examples of DNA microarray analysis based on the methodologies discussed in this paper.
Subject
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Topic
Statistics and Biostatistics
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Title
Rutgers University Electronic Theses and Dissertations
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ETD
Identifier
ETD_5469
PhysicalDescription
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electronic resource
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application/pdf
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text/xml
Extent
x, 113 p. : ill.
Note
(type = degree)
Ph.D.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = statement of responsibility)
by Ning Tang
Subject
(authority = ETD-LCSH)
Topic
DNA microarrays
Subject
(authority = ETD-LCSH)
Topic
Gene expression
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
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rucore19991600001
Location
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(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T31J982J
Genre
(authority = ExL-Esploro)
ETD doctoral
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Rights
RightsDeclaration
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The author owns the copyright to this work.
RightsHolder
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Name
FamilyName
Tang
GivenName
Ning
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
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(qualifier = exact);
(point = start)
2014-04-12 18:30:16
AssociatedEntity
Name
Ning Tang
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
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Type
License
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Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
RightsEvent
DateTime
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(qualifier = exact);
(point = start)
2014-05-31
DateTime
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2016-05-30
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after May 30th, 2016.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Technical
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ETD
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windows xp
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