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Expression profiling & functional genomics preprocessing Exercises

Expression profiling & functional genomics preprocessing Exercises. Database. Database. Database. Database. Database. Database. Database. Database. Database. Database. Database. Exercises. Array by array approach. Log transformation. Filtering. Normalisation. Ratio.

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Expression profiling & functional genomics preprocessing Exercises

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  1. Expression profiling & functional genomicspreprocessingExercises

  2. Database

  3. Database

  4. Database

  5. Database

  6. Database

  7. Database

  8. Database

  9. Database

  10. Database

  11. Database

  12. Database

  13. Exercises Array by array approach Log transformation Filtering Normalisation Ratio Test statistic (T-test)

  14. CyberT • Use the normalized data to find statistically differentially expressed genes: CyberT software • oefnbaldi.xls • http://visitor.ics.uci.edu/genex/cybert/ The file contain the 4 normalised ratios (see SNOMAD) T test on the ratios Array 1 Per gene, per condition 4 measurements available Paired samples Array 2

  15. Exercises • Dataset: mouse dataset • cDNA experiment:SNOMADtest2.txt • Analyze array1 by SNOMAD • Array by array normalization • ONE:measurements of the red channel • TWO: measurements of the green channel http://pevsnerlab.kennedykrieger.org/snomadinput.html http://www.bio.davidson.edu/courses/genomics/chip/chip.html

  16. SNOMAD http://pevsnerlab.kennedykrieger.org/snomadinput.html

  17. SNOMAD

  18. SNOMAD

  19. SNOMAD

  20. SNOMAD

  21. SNOMAD

  22. SNOMAD

  23. SNOMAD Results • Untransformed data • Note the multiplicative error • Note the influence of the Dye and condition effects

  24. SNOMAD Results • Linear normalisation of the untransformed data • Multiplicative effects still existing (not common) • Data after log transformation • Note the removal of the multiplicative error • Note the effect of the Dye and Condition • Note the non linear character of the data

  25. SNOMAD Results M/A plot M/A prior to normalisation

  26. SNOMAD Results Non linear lowess fit M/A after normalisation

  27. SNOMAD Results

  28. SNOMAD Results Original data Log transformed data Untransformed log ratio (M) Mean log intensity (A) Linearized log ratio CyberT

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