Question: Citing R, Bioconductor, and the affy package
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gravatar for Warnes, Gregory R
16.6 years ago by
Warnes, Gregory R460 wrote:
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, 299-314 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, 1996- I'm not sure about wheter or not to include H. Schwarte or whether the date is correct. For Bioconductor: ================ Paper: ------ 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: ===================== Paper: ------ 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? Thanks, -Greg LEGAL NOTICE\ Unless expressly stated otherwise, this message is... {{dropped}}
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ADD COMMENTlink modified 16.6 years ago by Vincent J. Carey, Jr.6.3k • written 16.6 years ago by Warnes, Gregory R460
Answer: Citing R, Bioconductor, and the affy package
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gravatar for Vincent J. Carey, Jr.
16.6 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
> 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.
ADD COMMENTlink written 16.6 years ago by Vincent J. Carey, Jr.6.3k
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