normalizationFactors {DESeq2} | R Documentation

## Accessor functions for the normalization factors in a DESeqDataSet object.

### Description

Gene-specific normalization factors for each sample can be provided as a matrix, which will preempt `sizeFactors`. In some experiments, counts for each sample have varying dependence on covariates, e.g. on GC-content for sequencing data run on different days, and in this case it makes sense to provide gene-specific factors for each sample rather than a single size factor.

### Usage

    normalizationFactors(object, ...)

    normalizationFactors(object, ...) <- value

    ## S4 method for signature 'DESeqDataSet'
    normalizationFactors(object)

    ## S4 replacement method for signature 'DESeqDataSet,matrix'
    normalizationFactors(object) <- value

### Arguments

`object` | a `DESeqDataSet` object.
`...` | additional arguments
`value` | the matrix of normalization factors

### Details

Normalization factors alter the model of `DESeq` in the following way, for counts K_ij and normalization factors NF_ij for gene i and sample j:

K_ij ~ NB(mu_ij, alpha_i)

mu_ij = NF_ij q_ij

### Note

Normalization factors are on the scale of the counts (similar to `sizeFactors`) and unlike offsets, which are typically on the scale of the predictors (in this case, log counts). Normalization factors should include library size normalization. They should have row-wise geometric mean near 1, as is the case with size factors, such that the mean of normalized counts is close to the mean of unnormalized counts. See example code below.

### Examples

    dds <- makeExampleDESeqDataSet(n=100, m=4)

    normFactors <- matrix(runif(nrow(dds)*ncol(dds),0.5,1.5),
                          ncol=ncol(dds),nrow=nrow(dds),
                          dimnames=list(1:nrow(dds),1:ncol(dds)))

    # the normalization factors matrix should not have 0's in it
    # it should have geometric mean near 1 for each row
    normFactors <- normFactors / exp(rowMeans(log(normFactors)))
    normalizationFactors(dds) <- normFactors

    dds <- DESeq(dds)

[Package DESeq2 version 1.20.0 Index]