| 09.Diagnostics {limma} | R Documentation |
This page gives an overview of the LIMMA functions available for microarray quality assessment and diagnostic plots.
This package provides an anova method which is designed for assessing the quality of an array series or of a normalization method.
It is not designed to assess differential expression of individual genes.
anova uses utility functions bwss and bwss.matrix.
The function arrayWeights estimates the empirical reliability of each array following a linear model fit.
Diagnostic plots can be produced by
imageplot imageplot3by2 will write imageplots to files, six plots to a page.plotFB plotMA plotMA3by2 will write MA-plots to files, six plots to a page.
mdplot can also be useful for comparing two one-channel microarrays.plotPrintTipLoess plotPrintorder plotDensities
plotPrintTipLoess uses utility functions gridr and gridc.
plotDensities uses utility function RG.MA.
Gordon Smyth