estimateSizeFactors: Estimate the size factors for a CountDataSet
In DESeq: Differential gene expression analysis based on the negative binomial distribution

Description Usage Arguments Details Value Author(s) See Also Examples

Estimate the size factors for a CountDataSet

1 2	## S4 method for signature 'CountDataSet' estimateSizeFactors( object, locfunc=median, ... )

`object`	a CountDataSet
`locfunc`	a function to compute a location for a sample. By default, the median is used. However, especially for low counts, the `shorth` may give better results.
`...`	extra arguments are ignored

You need to call this function right after newCountDataSet unless you have manually specified size factors.

Typically, the function is called with the idiom

cds <- estimateSizeFactors( cds )

This estimates the size factors and stores the information in the object.

Internally, the function calls estimateSizeFactorsForMatrix. See there for more details on the calculation.

The CountDataSet passed as parameters, with the size factors filled in.

Simon Anders, sanders@fs.tum.de

estimateSizeFactorsForMatrix

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cds <- makeExampleCountDataSet()
cds <- estimateSizeFactors( cds )
sizeFactors( cds )

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