QC and normalisation of microarray experiments - BiGCaT

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Red foreground intensity Green foreground intensity 10
Spot selection • Based on aspects as shown in the previous images, one can determine which spots to include <strong>and</strong> exclude from further analysis • Example criteria – Spot size (number <strong>of</strong> pixels) above threshold – Sufficient spot uniformity – No saturation – Above intensity threshold • For two channel arrays this may involve considering both channels together; this may be complicated 11
Page 1 and 2: QC and normalisation of microarray
Page 3 and 4: Quality Control
Page 5 and 6: QC • Quality control is an import
Page 7 and 8: Global array QC Foreground intensit
Page 9: Red number of pixels Green number o
Page 13 and 14: Further data preprocessing
Page 15 and 16: Background correction • Backgroun
Page 17 and 18: Normalisation procedures • Scale
Page 19 and 20: Why log two-color ratio data? (2 ch
Page 21 and 22: LogFC values after LOESS normalisat
Page 23 and 24: A QC module in Genepattern
Page 25 and 26: QC: what do the options mean? 1. Pr
Page 27 and 28: Image plot 27
Page 29 and 30: FitPLM residuals image 29
Page 31 and 32: Box- and whisker plot 31
Page 33 and 34: Normalised Unscaled Standard Error
Page 35 and 36: MA plot logFC= =average 35
Page 37 and 38: Correlation plot/heatmap 37
Page 39 and 40: A data preprocessing module in Gene
Page 41 and 42: NuGOExpressionFileCreator 41 • Pr
Page 43 and 44: Intermezzo: BrainArray CDF files 1
Page 45 and 46: The afternoon session • In the af
Page 47: Short description of the data set (

QC and normalisation of microarray experiments - BiGCaT

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