limmaAnalysis {birta} | R Documentation |
Needed for the parameterization of the model as well as the Fisher (pre-)test.
limmaAnalysis(dat, design, contrasts)
dat |
A matrix or ExpressionSet containing the expression values. |
design |
A design matrix. |
contrasts |
Contrast for the linear model. |
Returns a list containing the following entries:
pvalue.tab |
Containing the result of the topTable function from limma. |
lm.fit |
Linear fit to the model. |
design |
The design used. |
contrast |
The contrasts used. |
Benedikt Zacher (zacher@lmb.uni-muenchen.de), Holger Frohlich
G. K. Smyth. Limma : Linear Models for Microarray Data. Bioinformatics, (2005):397-420.
data(humanSim) design = model.matrix(~0+factor(c(rep("control", 5), rep("treated", 5)))) colnames(design) = c("control", "treated") contrasts = "treated - control" limmamRNA = limmaAnalysis(sim$dat.mRNA, design, contrasts)