[BioC] Citing R, Bioconductor, and the affy package

[Vincent Carey 525-2265]

> Paper: (as recommended in the R FAQ)
> ------
>
> R. Ihaka and R. Gentleman (1996), R: A Language for Data Analysis and
> Graphics, Journal of Computational and Graphical Statistics, Vol 5, No 3,
> 299-314

I continue to cite the above.  If the purpose is to notify
readers of literature relevant to the system, I would also
cite Chambers 1998 and Venables and Ripley 2002 because of their
scope.

>
> Paper:
> ------
>
> The FAQ suggests the R paper, but is there not a better publication?

It is now possible to cite

Gentleman R, Carey VJ. Visualization
and annotation of genomic experiments, in
Parmigiani G, Garrett ES, Irizarry RA, Zeger SL, eds.
The Analysis of Gene Expression Data, NY: Springer, 2003.
(I do not have the page numbers.)

This covers the project aims; there are chapters
by Rafael and Sandrine in the Parmigiani volume
that will likely also be relevant
to cite.

Thanks for checking -- we should update the FAQ to reflect these
pubs.