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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. - PowerPoint PPT Presentation
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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