Evalutating Biological Data Using Rank Correlation Methods

Analyses based upon rank correlation methods, such as Spearman's Rho and Kendall's Tau, can provide quick insights into large biological data sets. Comparing expression levels between different technologies and models is problematic due to the different units of measure. Here again, rank correlation provides an effective means of comparison between the two techniques. Massively Parallel Signature Sequencing (MPSS) transcript abundance levels to microarray signal intensities for Arabidopsis thaliana are compared. Rank correlations can be applied to subsets as well as the entire set. Results of subset comparisons can be used to improve the capabilities of predictive models, such as Predicted Highly Expressed (PHX). This is done for Escherichia coli. Methods are given to combine predictive models based upon feedback from experimental data. The problem of feature selection in supervised learning situations is also considered, where all features are drawn from a common domain and are best interpreted via ordinal comparisons with other features, rather than as numerical values. This is done for synthetic data as well as for microarray experiments examining the life cycle of Drosophila melanogaster and human leukemia cells. Two novel methods are presented based upon Rho and Tau, and their efficacy is tested with synthetic and real world data. The method based upon Spearman's Rho is shown to be more effective.

Name thesis:degree_name

Ph. D.

Level thesis:degree_level

doctoral

Discipline thesis:degree_discipline

Computer Science

Department dc:contributor.department

Computer Science

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2005

Author dc:creator

• Slotta, Douglas J.

Chair dc:contributor.committeechair

• Heath, Lenwood S.

Committee members dc:contributor.committeemember

• Ramakrishnan, Naren
• Murali, T. M.
• Vergara, John Paul C.
• Potts, Malcolm
• Helm, Richard F.

• MPSS
• bioinformatics
• microarrays
• spoiler count
• rank-order
• feature selection

Statement dc:rights

• In Copyright

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Dc Identifier Other

etd-05092005-105158

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/27613