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