exprs

reference


  This data set is part of a quality control study for tiling
  microarrays (Johnson et al., 2008), in which spike-ins were used to
  assess the influence of microarray platforms, preparation procedures,
  and analysis algorithms on the accuracy and reproducibility of
  ChIP-chip experiments. Here, the expression intensities of one region
  from the 'undiluted' data set investigated with Affymetrix arrays is
  selected, consisting of 452 probes and two conditions with three
  replicates each. The data has been normalized using quantile
  normalization and probe positions remapped to a common reference.


datasets

spikeInData

The 'les' package estimates Loci of Enhanced Significance
(LES) in tiling microarray data. These are regions of
regulation such as found in differential transcription,
CHiP-chip, or DNA modification analysis. The package provides a
universal framework suitable for identifying differential
effects in tiling microarray data sets, and is independent of
the underlying statistics at the level of single probes.

Julian Gehring

Identifying Differential Effects in Tiling Microarray Data

spikeInData function

<dl>
    <dt>exprs</dt><dd>Matrix with expression intensities, with rows
      representing probes and columns arrays. The names of the rows and
      columns contain the probe position and the treatment,
      respectively.</dd> <dt>pval</dt><dd>Vector with p-values assessing the differential effect
      between the conditions with a modified t-test. For details, please
      see the vignette of this package.</dd> <dt>reference</dt><dd>Data frame containing the location of the
      spike-in.</dd> </dl> 

Format

GEO accession IDs: GSM248996, ..., GSM249001

Source

This data set is part of a quality control study for tiling
  microarrays (Johnson et al., 2008), in which spike-ins were used to
  assess the influence of microarray platforms, preparation procedures,
  and analysis algorithms on the accuracy and reproducibility of
  ChIP-chip experiments. Here, the expression intensities of one region
  from the 'undiluted' data set investigated with Affymetrix arrays is
  selected, consisting of 452 probes and two conditions with three
  replicates each. The data has been normalized using quantile
  normalization and probe positions remapped to a common reference.

spikeInData: Spike-in ChIP-chip data set

Description

Usage

Arguments

Format

Source

References