Daniele Merico - HowTo Directory

Affymetrix Microarray Analysis

Importing raw data and generating standard gene expression metrics (signals, calls, etc...)

• [:DanieleMerico/HowtoDirectory/AffyCelCalSig: Importing Affymetrix CEL files, calculating MAS5 calls and signals]BR CEL files are the almost-raw files generated after chip image processing by Affymetrix software; BR the "fun" usually starts from the CEL files onwards; here's is the simplest things you can do with CEL files.

• [:DanieleMerico/HowtoDirectory/ExprSet: Importing Affymetrix CEL files, bothering about the R exprSet object, calculating MAS5 calls and signals]BR if the experimental design is quite complex, or you are using a function requiring an expression set (exprSet),BR then, sorry, but you probably need to read this part instead of the previous one.

Computing Differential Expression

• 2-class methods BR these methods require a dicotomic classification of the samples (e.g. case vs control), and reproducibility of samples belonging to the same class

  • [:DanieleMerico/HowtoDirectory/PLGEM: PLGEM]BR PLGEM is an error-model based method; it is recommended when the number of replicates is uneven between case and control; it has been successfully applied to tandem mass-spec proteomics data, where the signal was generated as abundancy-normalized peptide counts (NSAF)

    • Pubmed.ID: 15606915 (main)
    • Pubmed.ID: 18029349 (proteomic application)
  • SAM

General Computational Techniques

Computational Techniques for multi-dimensional data:

• [:DanieleMerico/HowtoDirectory/Distances: A few tips on distances] (especially for binary strings)