Difference between revisions of "Limma analysis"
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=Linear models for microarray analysis= | =Linear models for microarray analysis= | ||
Linear models for microarray analysis (''Limma'') is a [http://cran.stat.auckland.ac.nz/src/contrib/Descriptions/limma.html R] and [http://www.bioconductor.org/packages/1.8/bioc/html/limma.html Bioconductor] package for organising and analysing cDNA and Affymetrix microarray data. It is written by Gordon Smyth at WEHI. | Linear models for microarray analysis (''Limma'') is a [http://cran.stat.auckland.ac.nz/src/contrib/Descriptions/limma.html R] and [http://www.bioconductor.org/packages/1.8/bioc/html/limma.html Bioconductor] package for organising and analysing cDNA and Affymetrix microarray data. It is written by Gordon Smyth at WEHI. | ||
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| + | ==Algorithm details== | ||
| + | For a ''p'' * ''n'' matrix of expression intensities, ''Limma'' is fitting ''p'' linear models (one for each row). The lmFit function does this by calling functions such as ''lm.series'' | ||
| + | which use ''lm.fit'' in ''Package:Stats''. For cDNA/oligo two spotted technologies the matrix of expression intensities is usually the marix ''M'' values with respect to treatments. For Affymetrix single channel arrays the expression intensities are directly analysed comparing two treatments. | ||
Revision as of 21:35, 19 July 2006
Linear models for microarray analysis
Linear models for microarray analysis (Limma) is a R and Bioconductor package for organising and analysing cDNA and Affymetrix microarray data. It is written by Gordon Smyth at WEHI.
Algorithm details
For a p * n matrix of expression intensities, Limma is fitting p linear models (one for each row). The lmFit function does this by calling functions such as lm.series which use lm.fit in Package:Stats. For cDNA/oligo two spotted technologies the matrix of expression intensities is usually the marix M values with respect to treatments. For Affymetrix single channel arrays the expression intensities are directly analysed comparing two treatments.
