GEO—Gene Expression Omnibus
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Transcript of GEO—Gene Expression Omnibus
GEO—Gene Expression Omnibus
IBGP705
TA: Lee Cooper
February 18, 2009
Today’s lab
• Complete tutorial
• Email answers to questions to TA by 6pm today
Today’s lab
• Accessing GEO
• GEO Datasets
• GEO Profiles
• The “Help” Section
• BRB Array Tools
Preparing and carrying out a microarray experiment
Analysis of microarray data: clustering
Potential problems with microarray
Dealing with microarray problems
• Best answer = normalization
• Selection of normalization method/s
• Software
• Core lab
Today’s lab: GEO
• Various ways to visually examine microarray data to determine special need for normalization/ initial quality of data
• Accessing GEO
• GEO Datasets
• GEO Profiles
• The “Help” Section
• BRB Array Tools
Accessing GEO
GEO Datasets
GEO Datasets (old interface)
GEO Datasets (new interface)
Check distribution (normalization) and experimental design
Clustering (Algorithms and Parameters)
GEO Datasets: Analysis
GEO Profiles
GEO Profiles
GEO Profiles
GEO Profiles
GEO Profiles
BRB Array Tools