Difference between revisions of "Linear models for Microarray analysis"
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===== Origin ===== | ===== Origin ===== | ||
| − | *Written and maintained by Gordon Smyth with contributions | + | *Written and maintained by Gordon Smyth with contributions From WEHI, Melbourne, Australia |
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*Software made public at the Australian Genstat Conference, Perth, in Dec 2002 | *Software made public at the Australian Genstat Conference, Perth, in Dec 2002 | ||
*Became available in the Bioconductor open source bioinformatics project April 2003 | *Became available in the Bioconductor open source bioinformatics project April 2003 | ||
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[[Image:Limma_versions.tiff|thumb|200px|Linear development cycle]] | [[Image:Limma_versions.tiff|thumb|200px|Linear development cycle]] | ||
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====Object orintated programming environment==== | ====Object orintated programming environment==== | ||
[[Image:OOP.tiff|thumb]] | [[Image:OOP.tiff|thumb]] | ||
Revision as of 04:34, 14 March 2006
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
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
