extractProbeAnno

probeAnnoFromRGList

an object that holds the data and the probe match
    positions, currently can only be of class <code>RGList</code>

object

in which format are the reporter match positions stored
    in the object; see details; currently only "agilent" is implemented

format

further arguments that are passed on to the function
    <code>posToProbeAnno</code>


  This function can be used to build a probeAnno object from the
  reporter match positions given in the  'genes' slot of an RGList if
  present, as is the case with some ChIP-chip microarray platforms,
  e.g. with certain Agilent ones after reading in the data with
  <code>read.maimages(...,"agilent")</code>.


manip

The package Ringo facilitates the primary analysis
of ChIP-chip data. The main functionalities of the package are
data read-in, quality assessment, data visualisation and
identification of genomic regions showing enrichment in ChIP-chip.
The package has functions to deal with two-color oligonucleotide
microarrays from NimbleGen used in ChIP-chip projects, but also
contains more general functions for ChIP-chip data analysis, given
that the data is supplied as RGList (raw)  or ExpressionSet (pre-
processed).
The package employs functions from various other packages of the
Bioconductor project and provides additional ChIP-chip-specific
and NimbleGen-specific functionalities.

J Toedling

Ringo

R Investigation of ChIP-chip Oligoarrays

extractProbeAnno function

This function can be used to build a probeAnno object from the
  reporter match positions given in the  'genes' slot of an RGList if
  present, as is the case with some ChIP-chip microarray platforms,
  e.g. with certain Agilent ones after reading in the data with
  <code>read.maimages(...,"agilent")</code>.

extractProbeAnno: Build probeAnno from match positions in an RGList

Description

Usage

Arguments

Value

Details

See Also