Rosaceae

Microarray analysis workshop

Time schedule: 8:30 - 10:30am, 11-12:30am (3.5 hours)

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Workflow

Introduction to microarray analysis (10mins)

• A flow diagram for analysis
• Recap of cDNA microarrays (slide 3)
• Microarray data issues (slide 4)
• Microarray data issues (continued)
  • Large amount of data (GPR/JPEG file size)
  • Subjective
  • Need a log of what was done so someone else can quickly reroduce the results
  • → Reproducible research (someone else can understand/reproduce the results) (McGintys talk)
• Analysis process

Bioconductor

• Bioconductor is an open source development software project
• Provides tools for analysis and comprehension of genomic data
• Extensively for Affymetrix and cDNA microarray technologies

• The project started in the autumn of 2001

• Includes 23 core collaborating developers

Bioconductor Goals

The broad goals of the project are:

• To enable sound and powerful statistical analyses in genomics
• To provide a computing platform that allows the rapid design and deployment of high-quality software
• To develop a computing environment for both biologists and statisticians
• Promote high-quality dynamic documentation and reproducible research

• R resources/contributed guides (including downloading)
• R tutorial of basics (objects/indexing/functions)

+R tasklist

• • tasks available from web which utilze example data available in R - object assignment, subsetting, plotting, mathematical functions, sorting etc (20 tasks?)
• Usage/interaction within environment
• Bioconductor resources/vignettes(including downloading)
• Bioconductor basics (any resources for limma out there?)

Brief about Limma (10-15 mins)

• Essentially t-statistics for each spot/gene
• Uses between gene information in moderated t-statistics
• Computationally fast/robust
• Handles missing information/use defined flag information
• benefits/limitations?
• FDR control? → ranking better than selecting cutoff

Analysis script (1+hours)

+Workshop.R