Microarray Analysis

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Microarrays and Normalization; Bioconductor

  • Between array and within array normalization
  • Concordance coefficients and their use in normalization
  • Data cleaning
  • Instructions for the use of Bioconductor to preprocess affydata
  • Microarray experimental set up and quantification of information available from microarray experiments
  • Numerical illustration for 4-6 with complete set of annotated R-commands
  • Transformation of data 

Statistical Inference Procedures in Comparative Experiments

  • Adjustments for Multiple hypotheses testing including false discovery rate
  • Statistical hypothesis testing
  • Moderated t-test and empirical Bayes approach of limma package of bioconductor
  • Numerical illustration for 2-8 with complete set of annotated R-commands.
  • One way ANOVA
  • Paired t-test
  • Tests for validating assumptions of t-test
  • Two sample t- test
  • Welch test
  • Wilcoxon rank sum test, signed rank test
  • Multivariate Techniques (Principal component analysis)
  • Clustering (Cluster analysis)