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 variances 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.