Package 'limma' - Bioconductor
Package 'limma' - Bioconductor
Package 'limma' - Bioconductor
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14 10.GeneSetTests<br />
plotPrintTipLoess Produces a grid of MA-plots, one for each print-tip group on an array, together<br />
with the corresponding lowess curve. Intended to help visualize print-tip loess normalization.<br />
plotPrintorder<br />
order.<br />
For an array, produces a scatter plot of log-ratios or log-intensities by print<br />
plotDensities Individual channel densities for one or more arrays. An essential plot to accompany<br />
between array normalization, especially quantile normalization.<br />
plotMDS Multidimensional scaling plot for a set of arrays. Useful for visualizing the relationship<br />
between the set of samples.<br />
plotSA Sigma vs A plot. After a linear model is fitted, this checks constancy of the variance with<br />
respect to intensity level.<br />
plotPrintTipLoess uses utility functions gridr and gridc. plotDensities uses utility function<br />
RG.MA.<br />
Author(s)<br />
Gordon Smyth<br />
10.GeneSetTests<br />
Topic: Gene Set Tests<br />
Description<br />
This page gives an overview of the LIMMA functions for gene set testing and pathway analysis.<br />
roast<br />
mroast<br />
camera<br />
romer<br />
Self-contained gene set testing for one set.<br />
Self-contained gene set testing for many sets.<br />
Competitive gene set testing.<br />
Gene set enrichment analysis.<br />
symbols2indices Convert gene sets consisting of vectors of symbols into a list of indices suitable<br />
for use in the above functions.<br />
alias2Symbol and alias2SymbolTable Convert gene symbols or aliases to current official symbols.<br />
topRomer<br />
Display results from romer tests as a top-table.<br />
geneSetTest or wilcoxGST Simple gene set testing based on gene or probe permutation.<br />
barcodeplot<br />
Enrichment plot of a gene set.
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