timecourse (version 1.44.0)

MArrayTC-class: Microarray Time Course Object- class

Description

A list-based class for storing the analysis results from the multivariate empirical Bayes models of differential expression for longitudinal replicated developmental microarray time course data. Objects are normally created by mb.long and mb.MANOVA.

Slots/Components

MArrayTC objects do not contain any slots (apart from .Data) but they should contain the following list components:

M:

input matrix of log-ratios or log-values of expression for a series of microarrays.

Objects may also contain the following optional components:

prop:

numeric value giving the proportion of differentially expressed genes.

nu:

numeric value containing the estimated amount of moderation.

Lambda:

the estimated Lambda.

Lambda1:

the estimated Lambda1.

eta:

the estimated prior scale parameter.

alpha:

the estimated common mean of the expected time course vector under the null.

alpha.d:

the estimated condition-specific means of the expected time course vectors under the alternative.

beta:

the estimated scale parameter for the common covariance matrix of the common expected time course vector under the null.

beta.d:

the estimated condition-specific scale parameters for the common covariance matrix of the expected time course vectors under the alternative.

percent:

numeric matrix containing the percent of moderation corresponding to each sample size for the longitudinal one- and two- sample problems.

size:

numeric vector or matrix containing the sample sizes for all genes corresponding to different biological conditions, when the latter are sorted in ascending order.

con.group:

numeric or character vector giving the biological condition group of each array. The $i_th$ element of con.group corresponds to the biological condition of the $i_th$ column of M.

rep.group:

numeric or character vector giving the replicate group of each array. The $i_th$ element of rep.group corresponds to the replicate of the $i_th$ column of M.

time.group:

numeric vector giving the time group of each array. The $i_th$ element of time.group corresponds to the time of the $i_th$ column of M.

HotellingT2:

numeric vector giving the $\tilde{T}^2$ statistics of differential expression.

MB:

numeric vector giving the MB-statistics of differential expression.

pos.HotellingT2:

numeric vector whose $i_th$ element corresponds to the index of the gene with ranking $i$ in HotellingT2.

pos.MB:

numeric vector whose $i_th$ element corresponds to the index of the gene with ranking $i$ in MB.

geneNames:

character vector giving gene names.

descriptions:

character vector giving gene descriptions.

Methods

MArrayTC extends the LargeDataObject class in package limma, and inherits a show method from there. The function plotProfile takes MArrayTC as the input argument.