\HeaderA{AffysTissue}{Affymetrix' CDF probe set pairs}{AffysTissue}
\methaliasA{AffysTissue.noBl}{AffysTissue}{AffysTissue.noBl}
\aliasA{AffysTissueMC}{AffysTissue}{AffysTissueMC}
\keyword{datasets}{AffysTissue}
\begin{Description}\relax
Affymetrix' CDF probe set pairs
\end{Description}
\begin{Usage}
\begin{verbatim}
data(AffysTissue)
data(AffysTissueMC)
data(AffysTissue.noBl)
\end{verbatim}
\end{Usage}
\begin{Format}\relax
These three data.frames contain data for Affymetrix' CDF's probe set pairs with Q75 >= 55.
The \code{pr} and \code{target} columns hold the names of probe set X and Y, respectively. 
Column \code{alSum} contains the Q75 value of the alignment scores of X's 
reporters to the transcript of Y. 
The \code{meant2hit} and \code{PSofTarget} columns contain respectively the gene locus 
the probe set was designed to target and the probe set ID of the off-target Y, 
according to Affymetrix (extracted from ATH1-121501\_annot.csv).
The \code{peCC} column holds the pairs' Pearson correlation coefficient calculated 
on their expression intensities in the Tissue dataset (data originally from AtgenExpress Project).

\code{AffysTissue} is data.frame that contains all Affymetrix' CDF's probe set pairs 
with Q75 >= 55.
\code{AffysTissueMC} holds a subset of the pairs in \code{AffysTissue}, namely those
whose metacorrelation coefficient is not NA are included. 
For \code{AffysTissue.noBl}, the pairs of \code{AffysTissue} that align to each 
other with BLAST in at least one direction with an E-value smaller than 10\^{-10} 
were omitted.
\end{Format}
\begin{Author}\relax
Tineke Casneuf \email{tine@ebi.ac.uk}
\end{Author}
\begin{References}\relax
Casneuf, Van de Peer and Huber (Submitted); 
AtgenExpress data used: Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M. Schoelkopf, B. Weigel, D., and Lohmann, J. (2005) A gene expression map of Arabidopsis development. Nature Genetics, 37, 501-506.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{CustomsTissue}{CustomsTissue}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(AffysTissue)
data(AffysTissueMC)
data(AffysTissue.noBl)

## see also the vignette
\end{ExampleCode}
\end{Examples}

