. Lc_paper=fr_fr, . Utf-8, . Lc_name=c, . Lc_address=c, and L. Lc_telephone=c, LC_IDENTIFICATION=C Base packages: base, datasets, graphics, grDevices, methods, splines, stats, utils Other packages: affy 1

A. Inc, Statistical Algorithms Description Document, 2002.

M. J. Alston, J. Seers, J. C. Hinton, and S. Lucchini, BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets, BMC Bioinformatics, vol.11, issue.1, p.73, 2010.
DOI : 10.1186/1471-2105-11-73

M. Dai, P. Wang, A. D. Boyd, G. Kostov, B. Athey et al., Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data, Nucleic Acids Research, vol.33, issue.20, p.175
DOI : 10.1093/nar/gni179

P. Du, W. A. Kibbe, and S. M. Lin, lumi: a pipeline for processing Illumina microarray, Bioinformatics, vol.24, issue.13, pp.1547-1548, 2008.
DOI : 10.1093/bioinformatics/btn224

S. Falcon and R. Gentleman, Using GOstats to test gene lists for GO term association, Bioinformatics, vol.23, issue.2, pp.257-265, 2007.
DOI : 10.1093/bioinformatics/btl567

W. Huber, V. Heydebreck, A. S-?-aøltmann, H. Poustka, A. Vingron et al., Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics, vol.18, issue.Suppl 1, pp.96-104, 2002.
DOI : 10.1093/bioinformatics/18.suppl_1.S96

R. A. Irizarry and B. Hobbs, Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, vol.4, issue.2, pp.249-254, 2003.
DOI : 10.1093/biostatistics/4.2.249

A. Kauflmann, R. Gentleman, and W. Huber, ArrayQualityMetrics-a bioconductor package for quality assessment of microarray data, Bioinformatics, vol.25, pp.3-415, 2009.

B. Marty, Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells, Breast Cancer Research, vol.22, issue.6, p.101, 2008.
DOI : 10.1093/bioinformatics/btl359

M. Slawski, M. Daumer, and A. L. Boulesteix, CMA ??? a comprehensive Bioconductor package for supervised classification with high dimensional data, BMC Bioinformatics, vol.9, issue.1
DOI : 10.1186/1471-2105-9-439

A. Subramanian, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. USA, pp.15545-15550
DOI : 10.1073/pnas.0506580102

G. K. Smyth and T. P. Speed, Normalization of cDNA microarray data, Methods, vol.31, issue.4, pp.265-273, 2003.
DOI : 10.1016/S1046-2023(03)00155-5

L. J. Van-'t-veer, Gene expression profiling predicts clinical outcome of breast cancer, Nature, vol.415, issue.6871, pp.530-536, 2002.
DOI : 10.1038/415530a

Z. Wu and R. A. Irizarry, A Model-Based Background Adjustment for Oligonucleotide Expression Arrays, Journal of the American Statistical Association, vol.99, issue.468, p.909, 2004.
DOI : 10.1198/016214504000000683