1. DNA Microarray Quality Control Carlo Colantuoni ccolantu@jhsph.edu 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 33 9600 MGC elements

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

9. Outlier Identification in Microarray Quality Control

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

25. 4 arrays: Raw Log Intensities

26. 4 arrays: Raw Linear Intensities

27. 1 array: Ratio v. Intensity

30. Print-tip Effect

31. Bad Plate Effect

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

44. AGE ?

52. RNA Quality

53. AGE Batch

54. Positive Controls in Microarray Quality Control

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