summarizeProbes

$n x p$ matrix with $n$
  probe sets and $p$ samples.

exprs

a matrix or data.frame with 2 columns. The
  colnames of mapping have to contain at least 'graphID'
  and 'probesetID'. These two columns define the mapping
  between the probe sets on the microarray and the nodes of
  the graph.

mapping

defines how several probe sets should be
  combined. One of <code>median</code>, <code>mean</code>,
  <code>foldChange</code> or <code>none</code>.

method

defines the grouping of samples. Only
  needed if <code>method</code> is <code>foldChange</code>.

groups

a matrix that represents the graph of
  the underlying biological network.

adjacency


  Summarize multiple probe sets targeting one gene into one
  value for that gene. On most microarays there will be
  more than one probe set for a gene. However, in the
  underlying network the gene will only be present one
  time. Therefore, in order to calculate a Gene(Page)Rank
  weight for this gene, all expression measurements have to
  be summarized.


pathClass is a collection of classification methods that
use information about feature connectivity in a biological
network as an additional source of information. This additional
knowledge is incorporated into the classification a priori.
Several authors have shown that this approach significantly
increases the classification performance.

summarizeProbes: Summarize probe sets

Description

Usage

Arguments

Value

Details