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| Standard Microarray Analysis: | === Affymetrix Microarray Analysis === Importing raw data and generating standard gene expression metrics (signals, calls, etc...) |
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| the "fun" usually starts from CEL files onwards; here's is the simplest things you can do with CEL files. | the "fun" usually starts from the CEL files onwards; here's is the simplest things you can do with CEL files. |
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| 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 === |
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)
- SAM
General Computational Techniques
Computational Techniques for multi-dimensional data:
- [:DanieleMerico/HowtoDirectory/Distances: A few tips on distances] (especially for binary strings)