Dear users, I'm preparing a manuscript which includes the use of R, Bioconductor and the Affy package. The citations that I have found are: 1.- R R: Development core team (2004). R: A language and enviroment for statistical computing. R foundation for statistical computing. Vienna, Austria. http://www.r-project.org 2.- Bioconductor Ihaka R and Gentleman R. R: A Language for Data Analysis and Graphics}. Journal of Computational and Graphical Statistics. 1996 (5)3:299-314. 3.- Affy package Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15 Or I should citate any other reference? Such as: Bioconductor: open software development for computational biology and bioinformatics Robert C Gentleman , Vincent J Carey , Douglas M Bates , Ben Bolstad , Marcel Dettling , Sandrine Dudoit , Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang and Jianhua Zhang Genome Biology 2004, 5:R80 Thank you for your time. Jordi Altirriba PhD student Hospital Clinic - Barcelona - Spain

Thanks for both asking and citing the software. Please substitute the Genome Biology paper (we need to update the FAQ) as a citation for Bioconductor. Otherwise, it looks correct to me.....although Rafael may have a better indication for affy. I would also like to mention that as of R 2.0.0 the citation function should report appropriate citations for R and all packages can create their own citation entry (check the man page). Users are encouraged to appropriately cite the software that they use. Robert On Tue, Oct 05, 2004 at 05:00:03PM +0200, Jordi Altirriba Guti?rrez wrote: > Dear users, > I'm preparing a manuscript which includes the use of R, Bioconductor and the > Affy package. > The citations that I have found are: > 1.- R > R: Development core team (2004). R: A language and enviroment for > statistical computing. R foundation for statistical computing. Vienna, > Austria. http://www.r-project.org > 2.- Bioconductor > Ihaka R and Gentleman R. R: A Language for Data Analysis and Graphics}. > Journal of Computational and Graphical Statistics. 1996 (5)3:299-314. > 3.- Affy package > Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, > Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip > probe level data Nucleic Acids Research 31(4):e15 > > Or I should citate any other reference? Such as: > Bioconductor: open software development for computational biology and > bioinformatics > Robert C Gentleman , Vincent J Carey , Douglas M Bates , Ben Bolstad , > Marcel Dettling , Sandrine Dudoit , Byron Ellis, Laurent Gautier, Yongchao > Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano > Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony > J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean > YH Yang and Jianhua Zhang > Genome Biology 2004, 5:R80 > > Thank you for your time. > > > Jordi Altirriba > PhD student > Hospital Clinic - Barcelona - Spain > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

Jordi Altirriba Guti?rrez wrote: > Dear users, > I'm preparing a manuscript which includes the use of R, Bioconductor and > the Affy package. > The citations that I have found are: > 1.- R > R: Development core team (2004). R: A language and enviroment for > statistical computing. R foundation for statistical computing. Vienna, > Austria. http://www.r-project.org > 2.- Bioconductor > Ihaka R and Gentleman R. R: A Language for Data Analysis and Graphics}. > Journal of Computational and Graphical Statistics. 1996 (5)3:299-314. > 3.- Affy package > Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. > Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix > GeneChip probe level data Nucleic Acids Research 31(4):e15 The citation for the affy package is: Gautier, Cope, Bolstad and Irizarry - Bioinformatics 2004 (as found in the vignette for the affy package). > Or I should citate any other reference? Such as: > Bioconductor: open software development for computational biology and > bioinformatics > Robert C Gentleman , Vincent J Carey , Douglas M Bates , Ben Bolstad , > Marcel Dettling , Sandrine Dudoit , Byron Ellis, Laurent Gautier, > Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, > Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin > Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon > Smyth, Luke Tierney, Jean YH Yang and Jianhua Zhang > Genome Biology 2004, 5:R80 > > Thank you for your time. > > > Jordi Altirriba > PhD student > Hospital Clinic - Barcelona - Spain > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Jordi, I think 1+2 are good references for R, the Genome Biology article is good for Bioconductor, and the generic reference for the affy package (rather than any of the particular methods it implements) would be Gautier L, Cope L, Bolstad BM, Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004 Feb 12;20(3):307-15. PMID: 14960456 I guess the latter depends on whether you want to cite the affy package, RMA, or both. Best wishes Wolfgang Jordi Altirriba Guti?rrez wrote: > Dear users, > I'm preparing a manuscript which includes the use of R, Bioconductor and > the Affy package. > The citations that I have found are: > 1.- R > R: Development core team (2004). R: A language and enviroment for > statistical computing. R foundation for statistical computing. Vienna, > Austria. http://www.r-project.org > 2.- Bioconductor > Ihaka R and Gentleman R. R: A Language for Data Analysis and Graphics}. > Journal of Computational and Graphical Statistics. 1996 (5)3:299-314. > 3.- Affy package > Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. > Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix > GeneChip probe level data Nucleic Acids Research 31(4):e15 > > Or I should citate any other reference? Such as: > Bioconductor: open software development for computational biology and > bioinformatics > Robert C Gentleman , Vincent J Carey , Douglas M Bates , Ben Bolstad , > Marcel Dettling , Sandrine Dudoit , Byron Ellis, Laurent Gautier, > Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, > Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin > Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon > Smyth, Luke Tierney, Jean YH Yang and Jianhua Zhang > Genome Biology 2004, 5:R80 > > Thank you for your time. > > > Jordi Altirriba > PhD student > Hospital Clinic - Barcelona - Spain > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.dkfz.de/abt0840/whuber