| MArrayLM-class {limma} | R Documentation |
A list-based class for storing the results of fitting gene-wise linear models to a batch of microarrays.
Objects are normally created by lmFit.
MArrayLM objects do not contain any slots (apart from .Data) but they should contain the following list components:
coefficients:matrix containing fitted coefficients or contrastsstdev.unscaled:matrix containing unscaled standard deviations of the coefficients or contrastssigma:numeric vector containing residual standard deviations for each genedf.residual:numeric vector containing residual degrees of freedom for each geneObjects may also contain the following optional components:
genes:data.frame containing gene names and annotationdesign:matrix of full column rankcontrasts:matrix defining contrasts of coefficients for which results are desireds2.prior:numeric value giving empirical Bayes estimated prior value for residual variancesdf.prior:numeric vector giving empirical Bayes estimated degrees of freedom associated with s2.prior for each genes2.post:numeric vector giving posterior residual variancest:matrix containing empirical Bayes t-statisticsvar.prior:numeric vector giving empirical Bayes estimated variance for each true coefficient
RGList objects will return dimensions and hence functions such as dim, nrow and ncol are defined.
MArrayLM objects inherit a show method from the virtual class LargeDataObject.
The functions ebayes and classifyTestsF accept MArrayLM objects as arguments.
Gordon Smyth
2.Classes gives an overview of all the classes defined by this package.