DNA Microarray Quality Control Carlo Colantuoni April 25, 2007.

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Presentation transcript:

DNA Microarray Quality Control Carlo Colantuoni April 25, 2007

OR …

How many different ways can we look at global expression data?

Microarray Quality Control Depends on Technology

NHGRI Microarray Core Facility - Abdel Elkalhoun Oligonucleotide : 2-color Glass : Fluorescence : 36K

Illumina Microarray Platform Oligonucleotides : Beads : 24K : High Redundancy

Nylon NIA cDNA microarray Core Facility P MGC elements

Affymetrix - short oligos : many 10,000’s

Outlier Identification in Microarray Quality Control

Microarray Pseudo Images: Intensity

Microarray Pseudo Images: Ratios

Images of probe level data This is the raw data

Images of probe level data Residuals (or weights) from probe level model fits show problem clearly

Artifact & Bias Removal in Microarray Quality Control

Intensities and Ratios Green Red Intensity Log Ratio

4 arrays: Raw Log Intensities

4 arrays: Raw Linear Intensities

1 array: Ratio v. Intensity

Print-tip Effect

Bad Plate Effect

Print Order Effect

Uncorrected Intensities: MDS Colored by Batch

Removing The Batch Effect Much Like Red:Green Analysis

Uncorrected Intensities: MDS Colored by Batch

Batch Subtracted Measures: MDS Colored by Batch

MDS of All Array Experiments: Subject Replicates

Hybridization Artifacts

AGE ?

RNA Quality

AGE Batch

Positive Controls in Microarray Quality Control

As Many Views As Possible: Combing many diverse data types/views to see effects Outliers Artifacts & Bias Positive Controls Dimension Reduction

NIMH Joel Kleinman Tom Hyde Danny Weinberger JHSPH Rafael Irizarry JHU Michela Gallagher NHGRI Abdel Elkalhoun NIA & NIDA Kevin Becker Bill Freed Elin Lehrman JMHI Akira Sawa