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== 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)