You are here:
Vanderbilt Biostatistics Wiki
>
Main Web
>
Seminars
>
ChenSeminarSept08
(26 Apr 2013,
JohnBock
)
(raw view)
E
dit
A
ttach
Department of Biostatistics Seminar/Workshop Series ---+ Supervised Principal Component Analysis for Gene Set Enrichment of Microarray Data ---++ Xi (Steven) Chen, !PhD ---+++ The Cleveland Clinic Foundation<br>Cleveland, Ohio ---+++ Wednesday, September 10, 1:45-2:55pm, MRBIII Conference Room 1220 ---+++ Intended Audience: Persons interested in applied statistics, statistical theory, epidemiology, health services research, clinical trials methodology, statistical computing, statistical graphics, R users or potential users Gene set analysis allows formal testing of subtle but coordinated changes in a group of genes, such as those defined by Gene Ontology or KEGG Pathway databases. We propose a new method for gene set analysis that is based on Principal Component Analysis of genes expression values in the gene set. PCA is an effective method for reducing high dimensionality and capture variations in gene expression values. However, one limitation with PCA is that the latent variable identified by the first principal component may be unrelated to outcome. In the proposed Supervised Principal Component (SPCA) model for gene set analysis, the principal components are estimated from a selected subset of genes that are associated with outcome. As outcome information is used in the gene selection step, this method is supervised, thus called the Supervised PCA model. Because of the gene selection step, test statistic in SPCA model can no longer be approximated well using t distribution. We propose a two-component mixture distribution based on Gumbel extreme value distributions to account for the gene selection step. We show the proposed method compares favorably to currently available gene set analysis methods using simulated and real microarray data.
E
dit
|
A
ttach
|
P
rint version
|
H
istory
: r2
<
r1
|
B
acklinks
|
V
iew topic
|
Edit
w
iki text
|
M
ore topic actions
Topic revision: r2 - 26 Apr 2013,
JohnBock
Main
Department Home Page
Biostatistics Graduate Program
Vanderbilt University Medical Center
Main Web
Main Web Home
Search
Recent Changes
Changes
Topic list
Biostatistics Webs
Archive
Main
Sandbox
System
Register
|
Log In
Copyright © 2013-2022 by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Vanderbilt Biostatistics Wiki?
Send feedback