rankIvariantNormalise {beadarray} | R Documentation |
Normalise expression matrix using rank invariant genes
rankInvariantNormalise(exprs, T)
exprs |
a matrix of expression values |
T |
A target distribution vector to normalise the data to. The default is NULL in which case the average quantiles are used |
Using the normalize.invariantset
function from the affy package,
we find a list of rank invariant genes whose rank does not change significantly
between the columns of exprs
. We then fit a normalising curve to each
array using the values of the rank invariant genes of the array and a target
distribution.
The target distribution may be specified by the user and by default is the vector of average quantiles across all arrays.
Matrix of normalised expression data with the same dimensions as exprs
.
Mark Dunning
data(BSData) BSData.ri = assayDataElementReplace(BSData, "exprs", rankInvariantNormalise(exprs(BSData)))