normalizeByReference {tilingArray} | R Documentation

## Probe-specific normalization of hybridization intensities from a short-oligo microarray

### Description

Adjust the hybridization intensities from a short oligo microarray for probe-specific response effect by using one or several reference hybridizations.

### Usage

    normalizeByReference(x, reference, pm, background, nrStrata=10,
      cutoffQuantile=0.05, plotFileNames, verbose=FALSE)

### Arguments

`x` | eSet containing the data to be normalized.
`reference` | eSet with the same number of features as `x`, containing the reference signal.
`pm` | indices specifying the perfect match features in `reference`. This can be either an integer vector with values between 1 and `nrow(exprs(reference))` or a logical vector.
`background` | indices specifying a set of background features in `x`. This can be either an integer vector with values between 1 and `nrow(exprs(x))` or a logical vector.
`nrStrata` | Integer (length 1), number of strata for the estimation of the background function.
`cutoffQuantile` | Numeric (length 1), the probes whose reference signal is below this quantile are thrown out.
`plotFileNames` | Character vector whose length is the same as the number of arrays in `x`. Optional, if missing, no plots are produced.
`verbose` | Logical of length 1, if `TRUE`, some messages about progress are printed.

### Details

The intensities in `x` are adjusted according to the reference values. For example, the reference values could be obtained by hybridizing a DNA sample to the array. The abundance of target is thus the same for all PM probes, and the intensities that are actually observed can be used for estimating the adjustment parameters. Since this only makes sense for the PM probes, NA values be returned for all other probes. The set of indices for background probes, `background`, is used for the estimation of the background correction.

### Value

A copy of `x` with the normalized intensities.

### Author(s)

W. Huber huber@ebi.ac.uk

### References

Transcript mapping with oligonucleotide high-density tiling arrays, W. Huber, J. Toedling, L. Steinmetz, preprint (2006).

### Examples

      ## see vignette assessNorm.Rnw in inst/scripts directory

[Package tilingArray version 1.10.0 Index]