\HeaderA{hyperG2Affy}{A List of Affymetrix IDs from GOIDs}{hyperG2Affy}
\keyword{manip}{hyperG2Affy}
\keyword{htest}{hyperG2Affy}
\begin{Description}\relax
Output a list of Affymetrix IDs associated with each significant GOID,
based on the output from hyperGtable.
\end{Description}
\begin{Usage}
\begin{verbatim}
hyperG2Affy(probids, lib, type = "MF", pvalue = 0.05, min.count = 10,
universe = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{probids}] A vector of Affymetrix probe IDs
\item[\code{lib}] An annotation package (e.g., \code{hgu95av2})
\item[\code{type}] One of "MF", "CC", "BP", indicating molecular function,
cellular component, or biological process, respectively.
\item[\code{pvalue}] The significance level used to choose GO terms
\item[\code{min.count}] The minimum number of a given GO term that must be
on the chip in order to choose that GO term. This protects against
very low p-values that result from the situation where there are
very few genes with a given GO term on the chip, but one or two are
found in the set of significant genes.
\item[\code{universe}] A character vector of unique Entrez Gene identifiers
or \code{NULL}.  This is the population (the urn) of the
Hypergeometric test.  When \code{NULL} (default), the population is
all Entrez Gene ids in the annotation package that have a GO term
annotation in the specified GO category (see \code{GOHyperG} for
more details).
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function \code{hyperGtable} will output a table listing a set of
GOIDs that are significantly over-represented in a set of significant
genes. The next logical step might be to look at the individual genes
that are represented by each GOID. This function will output the
Affymetrix IDs for each GOID in a list, which can then be used to
either output HTML tables using \code{probes2table}, or possibly just
output the gene names for each GOID.
\end{Details}
\begin{Value}
A named \code{list} with all the Affymetrix IDs associated with each
significant GOID.
\end{Value}
\begin{Author}\relax
James W. MacDonald <jmacdon@med.umich.edu>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
library("hgu95av2")
probids <- ls(hgu95av2GENENAME)[1:10]
hyperG2Affy(probids, "hgu95av2")
\end{ExampleCode}
\end{Examples}

