Usage
analyseMA( data, design, id, cmat, cinfo, padj=c("none","bonferroni","fdr"), tol=1e-06 )
Arguments
data
a matrix of size $G \times N$ containing the normalized and/or standardized
data to be analyzed, where G is the number of spots under investigation and N is the
number of arrays used in the experiment. The matrix should contain one row for each spot.
The matrix should contain as many columns as arrays involved in the experiment, such that
each column contains the data for one single array. The matrix should not contain any ID variables,
which are entered separately. Missing values should be entered as NA.
design
the design matrix of size $N \times (K+2)$, where K is the number of
experimental conditions. This is the design matrix X known from linear model theory and
its elements are typically 0, 1, or -1. A 0 means that the associated parameter does not
apply for the corresponding observation (i.e., row). The first two columns are reserved
for the two dyes and are usually filled up with 1 and -1, respectively.
id
an ID vector of length G for the identification of the spots.
cmat
a matrix describing the p experimental questions (contrasts) to be analysed in
the experiment. The matrix can be composed of vectorial contrasts (a single row of the
matrix) and of contrasts in matrix form (several rows of the matrix),
e.g. an $A \times B$ interaction effect in a $3 \times 2$ design. All
contrasts have to be combined into one matrix (using rbind for instance).
cinfo
a vector of length p describing the grouping of the contrast matrix rows in vector or matrix
form. E.g. if the design matrix contains three contrasts in vector form, cinfo =
rep(1,3), if it contains two vectorial contratst and one as matrix with three rows,
cinfo=c(1,1,3).
padj
a quoted string indicating the multiplicity adjustment that should be used.
"none" - no multiplicity adjustment, "bonferroni" - Bonferroni single step adjustment,
"fdr" - linear step-up procedure of Benjamini and Hochberg.
tol
A value indicating the tolerance for contrast estimability check