[BioC] Bioconductor 2.4 is released

[Steve Lianoglou]

Hi,

> Can you direct me to any good overall training materials for the
> bioconductor packages for gene expression analysis? I'm interested
> primarily in scripts and example data. I've done a fair amount of work
> with S+ArrayAnalyzer at the GUI level, but want to come up to speed at
> the command level.


Start with the "primer" vignette in the affy package:

R> library(affy)
R> openVignette()
Please select a vignette:

  1: affy - 1. Primer
  2: affy - 2. Built-in Processing Methods
  3: affy - 3. Custom Processing Methods
  4: affy - 4. Import Methods
  5: Biobase - An introduction to Biobase and ExpressionSets
  6: Biobase - Bioconductor Overview
  7: Biobase - esApply Introduction
  8: Biobase - Notes for eSet developers
  9: Biobase - Notes for writing introductory 'how to' documents
10: Biobase - quick views of eSet instances

Choose (1)

Also, for an overview of how to analyze differential expression, see  
the limma user guide:

R> library(limma)
R> limmaUsersGuide()

Lastly, I've never read it myself, but perhaps the "Bioconductor Caste  
Studies" book might be valuable:

http://www.bioconductor.org/pub/biocases/

HTH,
-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

Contact Info: http://cbio.mskcc.org/~lianos/contact