1 / 12

Direct calibration of microarray probes

This workshop by Alex Pozhitkov, Peter A. Noble, and Diethard Tautz in 2011 delves into the conundrum of signal intensity against variables such as GC content and sense/antisense strands. Their study confirms the unpredictability of rRNA hybridization tests and explores factors like overhangs, buffer composition, and melting temperatures in microarray analysis instruments. The research emphasizes the importance of calibration in detecting copy number variations and acknowledges the support from the Max Planck Society and Alabama State University.

drago
Télécharger la présentation

Direct calibration of microarray probes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Direct calibration of microarray probes Making a “DNA-meter” Alex Pozhitkov, Peter A. Noble, Diethard Tautz, Ploen Workshop, 2011.

  2. Conundrum • Signal intensity vs. GC • Signal intensity vs. DG0 • Sense vs. antisense (same genomic loci) R2=0.37 Confirms: Pozhitkov, et al (2006). Tests of rRNA hybridization … cannot be predicted. NAR 34, e66-e6

  3. Melting study • Overhangs • Buffer composition • Tm Sense vs. Tm antisense • Tm vs. Signal Intensity on the array

  4. Tm Antisense (0C) Tm Sense (0C) Melting Temperatures

  5. Microarray is an Instrument Instruments require calibration

  6. 800 5000 5000 4000 600 3000 400 2000 200 1000 8 6 2 0 4 8 6 2 0 4 “Good”, “Bad” and Noise Signal Intensity Concentration Individual replicas Averages

  7. Freundlich isotherm!y=axb Langmuir isotherm is not the only possible isotherm: Pozhitkov et al. (2010) Beyond Affymetrix arrays: … NAR 38, e28.

  8. DNA and RNA y=axb+c

  9. Measurements and Errors Single probe replicate Average over 10 replicates

  10. CNV detection CNV expected: 1

  11. Sample prep variability $  loci

  12. Acknowledgements • Max Planck Society • Alabama State University

More Related