readNimblegen

Name of the file describing the arrays. In
    <code>limma</code> this file would be called targets file.

hybesFile

spot types also used by <code>limma</code>

spotTypesFile

Path to directoy that hold the files <code>hybesFile</code>,
    <code>spotTypesFile</code> and also the intensity files. Set this to
    <code>NULL</code> if you prefer the arguments <code>hybesFile</code>,
    <code>spotTypesFile</code> and the file-name entries of the hybes file to 
    be treated as absolute or relative file paths themselves.

path

string; pattern used to identify explantory
    header lines in the supplied pair-format files

headerPattern

verbose

further arguments passed on the <code>readNgIntensitiesTxt</code>


  Function to read in Nimblegen Intensity Text Files into an
  <code>RGList</code>. Calls some other functions for actual reading of data.
  This function is to be used with two-color NimbleGen array data.
  Use the function <code>read.xysfiles</code> of the <code>oligo</code> package
  for single-color data.


file

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

readNimblegen function

Function to read in Nimblegen Intensity Text Files into an
  <code>RGList</code>. Calls some other functions for actual reading of data.
  This function is to be used with two-color NimbleGen array data.
  Use the function <code>read.xysfiles</code> of the <code>oligo</code> package
  for single-color data.

readNimblegen: Function to read in Nimblegen Intensity Text Files

Description

Usage

Arguments

Value

See Also

Examples