Sample A: Cover Page of Thesis, Project, or Dissertation Proposal
Sample A: Cover Page of Thesis, Project, or Dissertation Proposal
Sample A: Cover Page of Thesis, Project, or Dissertation Proposal
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TABLE OF CONTENTS<br />
LIST OF TABLES .................................................................................................................................... viii<br />
LIST OF FIGURES .....................................................................................................................................ix<br />
ABSTRACT ...................................................................................................................................................x<br />
Chapter 1: An Introduction to Microarrays..............................................................................................1<br />
Microarrays: Hybridization and Signal .....................................................................................................4<br />
<strong>Page</strong><br />
Fact<strong>or</strong>s influencing Signal Interpretation ...................................................................................................5<br />
Hybridization Fact<strong>or</strong>s..............................................................................................................................5<br />
Dye-related Fact<strong>or</strong>s .................................................................................................................................8<br />
Gene Structure Fact<strong>or</strong>s ............................................................................................................................9<br />
Commonly Recognized Confounding Fact<strong>or</strong>s.........................................................................................9<br />
Background Contributions.....................................................................................................................10<br />
Microarray Platf<strong>or</strong>ms................................................................................................................................14<br />
Affymetrix U95 Platf<strong>or</strong>m ......................................................................................................................16<br />
Data Analysis and the Impact <strong>of</strong> the Data Cleansing Methods on Interpretation.....................................18<br />
Specific Aims .............................................................................................................................................21<br />
Summary....................................................................................................................................................24<br />
Chapter 2: The BaFL Pipeline ..................................................................................................................26<br />
Black Box Strategies .............................................................................................................................28<br />
Materials and Methods..............................................................................................................................30<br />
Hardware and S<strong>of</strong>tware.........................................................................................................................30<br />
Datasets .................................................................................................................................................31<br />
BaFL Pipeline Components...................................................................................................................32<br />
A Pri<strong>or</strong>i Prediction.................................................................................................................................40<br />
Results .......................................................................................................................................................41<br />
Probe Filtering Output...........................................................................................................................42<br />
Filter Effects..........................................................................................................................................44<br />
Array-Batch Results ..............................................................................................................................46<br />
ProbeSet Assessment Results................................................................................................................51<br />
Consistency <strong>of</strong> Probe Response.............................................................................................................51<br />
Potential Uncharacterized Transcript Events.........................................................................................53<br />
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