It is possible. You can make a column from a different table available on the fly using
\pgfplotstableset{
create on use/<new column name>/.style={
create col/copy column from table={<file or table>}{<column name>}
}
}
So, to get something like
you could do something like
\documentclass{article}
\usepackage{filecontents}
\begin{filecontents}{data.dat}
X Y
1 3
2 7
3 4
4 5
5 5
6 9
\end{filecontents}
\begin{filecontents}{error.dat}
Errors
1
3
2
2.5
3
1
\end{filecontents}
\usepackage{pgfplots,pgfplotstable}
\pgfplotstableread{data.dat}\datatable
\pgfplotstableset{
create on use/errors/.style={
create col/copy column from table={error.dat}{Errors}
}
}
\begin{document}
\begin{tikzpicture}
\begin{axis}[xmin=0,ymin=0]
\addplot +[
black,
error bars/.cd,
y explicit,
y dir=both
] table [y error=errors] {\datatable};
\end{axis}
\end{tikzpicture}
\end{document}