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DNA Microarray Quality Control Carlo Colantuoni April 25, 2007.

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Presentation on theme: "DNA Microarray Quality Control Carlo Colantuoni April 25, 2007."— Presentation transcript:

1 DNA Microarray Quality Control Carlo Colantuoni April 25, 2007

2 OR …

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

4 Microarray Quality Control Depends on Technology

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

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

7 Nylon NIA cDNA microarray Core Facility P MGC elements

8 Affymetrix - short oligos : many 10,000’s

9 Outlier Identification in Microarray Quality Control

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17 Microarray Pseudo Images: Intensity

18 Microarray Pseudo Images: Ratios

19 Images of probe level data This is the raw data

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

21 Artifact & Bias Removal in Microarray Quality Control

22 Intensities and Ratios Green Red Intensity Log Ratio

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25 4 arrays: Raw Log Intensities

26 4 arrays: Raw Linear Intensities

27 1 array: Ratio v. Intensity

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30 Print-tip Effect

31 Bad Plate Effect

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33 Print Order Effect

34 Uncorrected Intensities: MDS Colored by Batch

35 Removing The Batch Effect Much Like Red:Green Analysis

36 Uncorrected Intensities: MDS Colored by Batch

37 Batch Subtracted Measures: MDS Colored by Batch

38 MDS of All Array Experiments: Subject Replicates

39 Hybridization Artifacts

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44 AGE ?

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52 RNA Quality

53 AGE Batch

54 Positive Controls in Microarray Quality Control

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

65 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

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