\HeaderA{get.annotation}{Get annotation data for a gene list}{get.annotation}
\aliasA{results.summary}{get.annotation}{results.summary}
\aliasA{write.annotation}{get.annotation}{write.annotation}
\keyword{misc}{get.annotation}
\begin{Description}\relax
Takes a vector of probeset names and a CDF name. Produces a table of
annotations, containing gene name, description, sequence accession
number and unigene accession number for each probeset. In addition,
write.annotation is a utility function that outputs the annotation
data in a form suitable for loading into excel and results.summary
takes the outut of pairwise.comparison or pairwise.filter and spits
out a table with the means of the replicates the fold-change between
them (log2) and t-test p-values. This is followed by a table of
annotation (produced by get.annotation).
\end{Description}
\begin{Usage}
\begin{verbatim}
get.annotation(x, cdfname,verbose=FALSE)
write.annotation(summary,file="results/annotation.table.xls")
results.summary(results,cdfname)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a vector of probe names 
\item[\code{cdfname}] the name of the chip (as produced by cdfName(AffyBatch) 
\item[\code{verbose}] print out information if problems are found looking things up in the annotation data 
\item[\code{summary}] a table of data to write in a format appropriate to read into Excel 
\item[\code{file}] a table delimited file 
\item[\code{results}] a PairComp object, as produced by pairwise.comparison and pairwise.filter 
\end{ldescription}
\end{Arguments}
\begin{Value}
A table containing annotation data
\end{Value}
\begin{Author}\relax
Crispin J Miller
\end{Author}
\begin{References}\relax
http://bioinformatics.picr.man.ac.uk/
\end{References}
\begin{Examples}
\begin{ExampleCode}
 ## Not run: 
   pw       <- pairwise.comparison(eset.rma,"group",c("A","P"))
   pw.filtered <- pairwise.filter(pw)
   summary     <- results.summary(pw.filtered,"hgu133a")
   write.annotation(file="spreadsheet.xls",summary)
  
## End(Not run)
\end{ExampleCode}
\end{Examples}