fitQuantileNormFcn.AffymetrixCelFile

AffymetrixCelFile.fitQuantileNormFcn

fitQuantileNormFcn,AffymetrixCelFile-method

yTarget

An optional <code><a href="/link/numeric?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a href="/link/vector?package=aroma.affymetrix&version=2.11.1&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> specifying the indices of the
     subset of probes to be used to fit the normalization function.

subset

Control parameters passed to
     <code><a href="/link/smooth.spline?package=aroma.affymetrix&version=2.11.1&to=stats" rd-options="stats" data-mini-rdoc="stats::smooth.spline">smooth.spline</a></code>.

spar, nknots

See <code><a href="/link/Verbose?package=aroma.affymetrix&version=2.11.1&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Fits quantile normalization functions for the arrays in the data set.

methods

internal

This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.  These are designed to be memory efficient but still being fast.  The idea is to keep all data on file and only read data into memory when needed.  Clever caching mechanisms are used to minimize the overhead of data IO.  All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory.  With this design it is only the disk space that limits the number of arrays that can be analyzed.

fitQuantileNormFcn.AffymetrixCelFile: Fits quantile normalization functions for the arrays in the data set

Description

Usage

Arguments

Value

See Also