DKMshift | R Documentation |
Low level routine to apply the DKM background correction step of RMA
DKMshift(m, target = getGlobalMetrics(obj)$DKM)
m |
numeric matrix of expression data, with a row for each gene/oligo, and a column for each sample |
target |
target value for the mode of the density kernel for each column |
This function implements the background subtraction step of RMA. It
prevents the creation of negative expression values, by a linear
compaction of values smaller than target
.
a numeric matrix of the same size as m
, with the background
correction linear shift applied to all columns
duffyRMA
, for details about the RMA implementation.
getDensityKernelMode
, for calculating DKM.
getGlobalMetrics
, for various metrics of an expression matrix
including the mean DKM value.
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