Description Slots/Components Methods Author(s)

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`

.

`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.

MArrayTC extends the
`LargeDataObject`

class in package limma, and
inherits a `show`

method from there.

The function `plotProfile`

takes `MArrayTC`

as the input argument.

Yu Chuan Tai yuchuan@stat.berkeley.edu

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