kidney

Intensity data for 1 cDNA slide with two adjacent tissue samples
  from a nephrectomy (kidney)

datasets

The package implements a method for normalising microarray intensities,
both between colours within array, and between arrays. The method uses a
robust variant of the maximum-likelihood estimator for the stochastic model of
microarray data described in the references (see vignette).
The model incorporates data calibration (a.k.a. normalization), a model for
the dependence of the variance on the mean intensity, and a
variance stabilizing data transformation. Differences between
transformed intensities are analogous to "normalized
log-ratios". However, in contrast to the latter, their
variance is independent of the mean, and they are usually more
sensitive and specific in detecting differential
transcription.

Wolfgang Huber

Variance stabilization and calibration for microarray data

kidney function

<code>kidney</code> is an
  <code><a rd-options="Biobase:class.ExpressionSet" href="/link/ExpressionSet?package=vsn&version=3.40.0&to=Biobase%3Aclass.ExpressionSet" data-mini-rdoc="Biobase:class.ExpressionSet::ExpressionSet">ExpressionSet</a></code>
  containing the data from one cDNA
  chip. The 8704x2 matrix <code>exprs(kidney)</code> contains the
  spot intensities for the red (635 nm) and green color channels
  (532 nm) respectively. For each spot, a background estimate from a
  surrounding region was subtracted.

Format

<code>kidney</code> is an
  <code><a rd-options='Biobase:class.ExpressionSet' href='ExpressionSet'>ExpressionSet</a></code>
  containing the data from one cDNA
  chip. The 8704x2 matrix <code>exprs(kidney)</code> contains the
  spot intensities for the red (635 nm) and green color channels
  (532 nm) respectively. For each spot, a background estimate from a
  surrounding region was subtracted.

kidney: Intensity data for 1 cDNA slide with two adjacent tissue samples from a nephrectomy (kidney)

Description

Usage

Arguments

Format

Details

References

See Also

Examples