[BioC] Citation of R, Bioconductor and Affy

[Wolfgang Huber]

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 Gutiérrez 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 at 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