Rosaceae

Microarray analysis workshop

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

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TODO - Split and linkify article

Workflow

1. Introduction to Microarray analysis (10mins - Marcus Davy)
2. Normalization (10mins - Robert Schaffer)
3. Bioconductor/R framework (15 mins - Marcus Davy
4. R Lab Tutorial (45mins)
5. Linear models for Microarray analysis (limma) (15 mins - Marcus Davy)
6. Experimental analysis ("45mins")

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+Bioconductor/R framework

+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

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Scratch pad

• 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

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