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

Warnes, Gregory R gregory_r_warnes at groton.pfizer.com
Fri Apr 18 10:16:07 MEST 2003

Hi All,

We'll be presenting a poster and then a paper for which I've performed the
data analysis using R, Bioconductor, and the affy package.  I want to cite
both a paper (so the authors get citation credit) and a web location (so
users  can find the code!) for each.  

I would appreciate some help getting the citations right.  

For R:

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,

Is there anything newer?

Web Site:

How about:

D. Bates, J. Chambers, P. Dalgaard, R. Gentleman, K. Hornik, S. Iacus, R.
Ihaka, F. Leisch, T. Lumley, M. Maechler, G. Masarotto, D. Murdoch, P.
Murrell, M. Plummer, B. Ripley, H. Schwarte, D. Temple Lang, L. Tierney, The
R Project for Statistical Computing (Web Site), http://www.r-project.org,

I'm not sure about wheter or not to include H. Schwarte or whether the date
is correct.

For Bioconductor:


The FAQ suggests the R paper, but is there not a better publication?  

Web Site:  

How about:

D. Bates, V. Carey, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, R.
Gentleman, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R.
Irizarry, F. Leisch, M. Maechler, A. Rossini, G. Sawitzki, L. Tierney,
J.Y.H. Yang, J. Zhang.  Bioconductor (Web Site),
http://www.bioconductor.org/, 2002-.

For the Affy package:


R. Irizarry, L. Gautier, and L. Cope. An r package for analyses of
affymetrix oligonucleotide arrays. In G. Parmigiani, E. S. Garrett, R. A.
Irizarry, and S. L. Zeger, editors, The Analysis of Gene Expression Data:
Methods and Software. Springer, New York, 2002. 

Web Site:

 ?just the bioconductor site?



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