duffyRMA | R Documentation |
Our local implementation of RMA normalization
duffyRMA(m, targetBGlevel = NULL, magnitudeScale = NULL, columnSets = list(all = 1:ncol(m)))
duffyMagnitudeNormalize(m, globalSum = 1000 * nrow(m))
duffyRMA.bgSubtract(m, targetBGlevel = NULL)
duffyRMA.qn(m, columnSets = list(all = 1:ncol(m)))
m |
numeric matrix of expression data, with one row per oligo/gene and one column per sample |
targetBGlevel |
background correction target value. |
magnitudeScale |
mean gene intensity target value (aka Quackenbush). |
columnSets |
a list of vectors of column numbers, to do RMA on subsets of columns of |
globalSum |
total sum of gene intensity target value (aka Quackenbush) |
This implementation of RMA gives more layers of flexibility. Global scaling in the style of Quackenbush (2002), with settable average gene intensity, is the first step. Next, the adjustment for background hybridization levels can be set to an explicit value, or calculated from the mode of the density kernel. Lastly, the quantile normalization step is run. Each of these functions is callable separately for finer control.
a matrix of the same size as m
, with normalized expression values
Bob Morrison
Irizarry, B. & Bolstad, B. (2003) Nucleic Acids Research 31(4):e15
getGlobalMetrics
, for various metrics of an expression matrix.
DKMshift
, for details on applying the density kernel mode
background correction.
rankEquivalentIntensity
, for simple quantile normalization.
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