Presentation on theme: "Quality control of Affymetrix arrays. What can go wrong? RNA degradation (before hyb) –3’/5’ Dirty samples –background, % present calls Uneven hybridizations."— Presentation transcript:
Solution Uneven hybridizations: normalization takes care of RNA degradation: outliers problematic High background: the results will not be as clear, but trends can still be seen –Bioinformatics and Computational Biology Soultions Using R and Bioconductor. Gentleman et al. Chapter 3: Quality assessment of Affymetrix GeneChip Data, Bolstad et al.
Machine problems With time, settings change which reflects on the data Roos Jahangir Tafrechi Arnolda de Nooij-van Dalen old vs old new vs old