Description Usage Arguments Value Author(s) See Also Examples
Given a matrix or data frame of count data, this function estimates the size
factors as follows: Each column is divided by the geometric means of the
rows. The median (or, if requested, another location estimator) of these
ratios (skipping the genes with a geometric mean of zero) is used as the size
factor for this column. Typically, one will not call this function directly, but use
estimateSizeFactors
.
1 2 3 4 5 6 7 
counts 
a matrix or data frame of counts, i.e., nonnegative integer values 
locfunc 
a function to compute a location for a sample. By default, the
median is used. However, especially for low counts, the

geoMeans 
by default this is not provided, and the geometric means of the counts are calculated within the function. A vector of geometric means from another count matrix can be provided for a "frozen" size factor calculation 
controlGenes 
optional, numeric or logical index vector specifying those genes to use for size factor estimation (e.g. housekeeping or spikein genes) 
type 
standard median ratio ( 
a vector with the estimates size factors, one element per column
Simon Anders
1 2 3 4  dds < makeExampleDESeqDataSet()
estimateSizeFactorsForMatrix(counts(dds))
geoMeans < exp(rowMeans(log(counts(dds))))
estimateSizeFactorsForMatrix(counts(dds),geoMeans=geoMeans)

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