It seems that xtable does not escape special characters such as % (which indicates a comment line in LaTeX).
 
Try these few lines for example:
> library(xtable)
> q<-data.frame(quantile(rnorm(100)))
> xtable(q)
 
This produces:

% latex table generated in R 1.9.1 by xtable 1.2-3 package
% Sat Aug 28 16:11:05 2004
\begin{table}[ht]
\begin{center}
\begin{tabular}{rr}
\hline
 & quantile.rnorm.100.. \\
\hline
0% & $-$2.02 \\
25% & $-$0.70 \\
50% & $-$0.16 \\
75% & 0.54 \\
100% & 2.16 \\
\hline
\end{tabular}
\end{center}
\end{table}
> 



		
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