Description Usage Arguments Details Value Author(s) References Examples
make.design.matrix
creates the design matrix of dummies for fitting time series micorarray
gene expression experiments.
1 2  make.design.matrix(edesign, degree = 2, time.col = 1,
repl.col = 2, group.cols = c(3:ncol(edesign)))

edesign 
matrix describing experimental design. Rows must be arrays and columns experiment descriptors 
degree 
the degree of the regression fit polynome. 
time.col 
column number in edesign containing time values. Default is first column 
repl.col 
column number in edesign containing coding for replicate arrays. Default is second column 
group.cols 
column numbers in edesign indicating the coding for each experimental group (treatment, tissue, ...). See details 
rownames of edesign object should contain the arrays naming (i.e. array1, array2, ...). colnames of edesign must contain the names of experiment descriptors(i.e. "Time", "Replicates", "Treatment A", "Treatment B", etc.). for each experimental group a different column must be present in edesign, coding with 1 and 0 whether each array belongs to that group or not.
make.design.matrix
returns a design matrix where rows represent arrays and column variables of time, dummies and their interactions for up to the degree
given.
Dummies show the relative effect of each experimental group related to the first one. Single dummies indicate the abcissa component of each group.
$Time*dummy$ variables indicate slope changes, $Time^2*dummy$ indicates curvature changes. Higher grade values could model complex responses.
In case experimental groups share a initial state (i.e. common time 0), no single dummies are modeled.
dis 
design matrix of dummies for fitting time series 
groups.vector 
vector coding the experimental group to which each variable belongs to 
edesign 

Ana Conesa and Maria Jose Nueda, mj.nueda@ua.es
Conesa, A., Nueda M.J., Alberto Ferrer, A., Talon, T. 2006. maSigPro: a Method to Identify Significant Differential Expression Profiles in TimeCourse Microarray Experiments. Bioinformatics 22, 10961102
1 2 3  data(edesign.abiotic, edesignCT)
make.design.matrix(edesign.abiotic) # quadratic model
make.design.matrix(edesignCT, degree = 3) # cubic model with common starting time point

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