Linear models for Microarray analysis
From Organic Design wiki
Overview of Limma package for R
- Fits a linear model for each spot (gene)
- An open source software package for the R programming environment
- Focus on normalization and statistical analysis of cDNA microarray gene expression data
- OOP environment for handling information in a microarray experiment
- Statistical analysis approach can be used for Affymetrix microarray experiments
Origin
- Written and maintained by Gordon Smyth with contributions From WEHI, Melbourne, Australia
- Software made public at the Australian Genstat Conference, Perth, in Dec 2002
- Became available in the Bioconductor open source bioinformatics project April 2003
- Limma integrates with other Bioconductor software packages, affy, marray, using convert package
- Active development cycle
Object orintated programming environment
- RGList automatically populates R, G, Rb, Gb, weights, genes elements from GPR slides
Scratchpad
- 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
