Rosaceae
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Contents
Microarray analysis workshop
Time schedule: 8:30 - 10:30am, 11-12:30am (3.5 hours)
Workflow
- Introduction to Microarray analysis (10mins - Marcus Davy)
- Normalization (10mins - Robert Schaffer)
- Bioconductor/R framework (15 mins - Marcus Davy)
- R tutorial (45mins)
- Linear models for Microarray analysis (limma) (15 mins - Marcus Davy)
- Experimental analysis ("45mins")
- 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
