affyPara - A bioconductor package for parallelized preprocessing algorithms of Affymetrix microarray data

Bioinformatics and Biology Insights

Volumn 2009, Issue 3, 2009, Pages 83-87

  Schmidberger, Markus ^a   Vicedo, Esmeralda ^a   Mansmann, Ulrich ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

Computing; Microarray; Normalization; Parallel; Preprocessing; R

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; INFORMATION PROCESSING; MATHEMATICAL MODEL; MICROARRAY ANALYSIS; PARALLEL DESIGN; PROBLEM SOLVING;

EID: 69849094662     PISSN: None     EISSN: 11779322     Source Type: Journal    
DOI: None     Document Type: Article

References (16)

1. Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005; Springer, 1 edition.
2. R Development Core Team R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. 2008.
3. Gentleman RC, Carey VJ, et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology. 2004;5.
4. Irizarry RA, Hobbs B, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Bio statistics. 2003;4(2):249-64.
5. Irizarry R, Gautier L, Cope L. An R package for analyses of affymetrix oligonucleotide arrays. In Parmigiani G, Garrett E, Irizarry R, and Zeger S, editors, The Analysis of Gene Expression Data: Methods and Software. 2002; Springer, New York.
6. Bolstad BM. Low-level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. 2004; Ph.D. thesis, University of California, Berkeley.
7. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002;18 Suppl 1: S96-104.
8. Schmidberger M, Mansmann U. Parallelized preprocessing algorithms for high-density oligonucleotide arrays. In Proc. IEEE International Symposium on Parallel and Distributed Processing IPDPS. 2008;1-7.
9. Ruschhaupt M, Huber W, Poustka AM, Mansmann U. A compendium to ensure computational reproducibility in high-dimensional classification tasks. SAGMB. 2004;3: Article 37.
10. Bacher U, Kohlmann A, Haferlach T. Current status of gene expression profiling in the diagnosis and management of acute leukaemia. Br J Haematol. 2009.
11. Kostka D, Spang R. Microarray based diagnosis profits from better documentation of gene expression signatures. PLoS Comput Biol. 2008; 4(2):e22.
12. Bengtsson H. Aroma M an R object-oriented microarray analysis environment. Preprints in Mathematical Sciences, Mathematical Statistics, Lund University. 2004;18.
13. Schmidberger M, Morgan M, Eddelbuettel D, Yu H, Tierney L, Mansmann U. State-of-the-art in parallel computing with R. Journal of Statistical Software. 2009; Accepted, 1-26.
14. Rossini AJ, Tierney L, Li NM. Simple parallel statistical computing in R. Journal of Computational and Graphical Statistics. 2007;16(2): 399-420.
15. Sloan J. High Performance Linux Clusters with OSCAR, Rocks, OpenMosix, and MPI (Nutshell Handbooks). O'Reilly Media, Inc 2004.
16. Amdahl GM. Validity of the single processor approach to achieving large scale computing capabilities. In AFIPS '67 (Spring): Proceedings of the April 18-20, 1967, spring joint computer conference, pages 483-5, New York, NY, USA. ACM.