QC and normalisation of microarray experiments - BiGCaT

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Quality Control Overview plot Default criteria: Percentage present within 10% Background within 20 units Scaling factors within 3-fold from the average GAPDH 3’/5’ ≤ 1.25 Actin 3’/5’ ≤ 3 26
Image plot 27
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 and 10: Red number of pixels Green number o
Page 11 and 12: Spot selection • Based on aspects
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: QC: what do the options mean? 1. Pr
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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