[1] D. Abdueva, D. Skvortsov and S. Tavar�, Non-linear analysis of GeneChip arrays, Nucleic Acids Res. 15 (2006), e1-7.

[2] Affymetrix, Affymetrix Microarray Suite User Guide, Version 4 ed., Affymetrix Santa Clara, CA., 1999.

[3] Affymetrix, Inc., Technical Note: GeneChip Arrays Provide Optimal Sensitivity and Specificity for Microarray Expression Analysis, 2001.

[4] Affymetrix, Inc., Statistical Algorithms Description Document, 2002.

[5] Affymetrix, Inc., Technical Note: Guide to Probe Logarithmic Intensity Error (PLIER) Estimation, 2005.

[6] D. B. Allison, X. Cui, G. P. Page and M. Sabripour, Microarray data analysis: from disarray to consolidation and consensus, Nature Rev. Genet. 7 (2006), 55-65.

[7] Z. Chen, M. McGee, Q. Liu and R. H. Scheuermann, A distribution free summarization method for Affymetrix GeneChip arrays, Bioinformatics 23 (2007), 321-327.

[8] S. E. Choe, M. Boutros, A. Michelson, G. M. Church and M. S. Halfon, Preferred analysis methods for Affymetrix GeneChip revealed by a wholly defined control dataset, Genome Biology 6 (2005), R16.

[9] L. M. Cope, R. A. Irizarry, H. A. Jaffee, Z. Wu and T. P. Speed, A benchmark for Affymetrix GeneChip expression measures, Bioinformatics 20 (2004), 323-331.

[10] L. Gautier, L. Cope, B. M. Bolstad and R. A. Irizarry, Affy-analysis of Affymetrix GeneChip data at the probe level, Bioinformatics 20(3) (2004), 307-315.

[11] B. Harr and C. Schlotterer, Comparisons of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons, Nucleic Acids Res. 34(2) (2006), e8.

[12] S. Hochreiter, D. Clevert and K. Obermayer, A new summarization method for Affymetrix probe level data, Bioinformatics 22(8) (2006), 943-949.

[13] R. A. Irizarry, B. M. Bolstad, F. Collin, L. M. Cope, B. Hobbs and T. P. Speed, Summaries of Affymetrix GeneChip probe level data, Nucleic Acids Res. 31(4) (2003), e15.

[14] R. A. Irizarry, B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf and T. P. Speed, Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics 4 (2003), 249-264.

[15] R. A. Irizarry, Z. Wu and H. A. Jaffee, Comparison of Affymetrix GeneChip expression measures, Bioinformatics 1(1) (2005), 1-7.

[16] S. Katz, R. A. Irizarry, X. Lin, M. Tripputi and M. W. Porter, A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database, BMC Bioinformatics 7 (2006), 464.

[17] S. Kullback and R. A. Leibler, On information and sufficiency, Ann. Math. Statist. 22 (1951), 79-86.

[18] C. Li and W. H. Wong, Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection, Proc. Natl. Acad. Sci. USA 98(1) (2001a), 31-36.

[19] C. Li and W. H. Wong, Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application, Genome Biol. 2 (2001b), 1-11.

[20] R. Lipshutz, S. Fodor, T. Gingeras and D. Lockenhart, High density synthetic oligonucleotidearrays, Nature Genet. 21(Suppl.) (1999), 20-24.

[21] F. F. Millenaar, J. Okyere, S. T. May, M. V. Zanten, L. ACJ. Voesenek and A. JM. Peeters, How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results, BMC Bioinformatics 7 (2006), 137.

[22] F. Naef, D. A. Lim, N. Pantil and M. A. Magnasco, From features to expression: high-density oligonucleotide array analysis revisited, Technical Report 1 (2001), 1-9.

[23] M. Ohtaki, K. Otani, K. Satoh, T. Kawamura, K. Hiyama and M. Nishiyama, Model-based analysis of microarray data: expression of differentially expressed genes between two cell types based on a two-dimensional mixed normal model, Jpn. J. Biometrics 26(1) (2005), 31-48.

[24] C. R. Rao, Linear Statistical Inference and its Applications, 2nd ed., John Wiley & Sons, New York, 1973.

[25] J. Seo and E. P. Hoffman, Probe set algorithms: is there a rational best bet?, BMC Bioinformatics 7 (2006), 395.

[26] Z. Wu and R. A. Irizarry, Preprocessing of oligonucleotide array data, Nature Biotechnology 22 (2004), 656-658.

[27] C. Wu, R. Carta and L. Zhang, Sequence dependence of cross-hybridization on short oligo microarrays, Nucleic Acids. Res. 33(9) (2005), e84.

[28] Z. Wu and R. Irizarry, Stochastic methods inspired by hybridization theory for short oligonucleotide arrays, J. Comut. Biol. 12 (2005), 882-893.

[29] Z. Wu, R. Irizarry, R. Gentleman, F. Martinez-Murrillo and F. Sprencer, A model-based background adjustment for oligonucleotide expression arrays, J. Amer. Statist. Assoc. 99 (2004), 909-917.

[30] L. Zhang, M. Miles and K. D. Aldape, A mode of molecular interaction on short oligonucleotide microarrays, Nature Biotechnology 21 (2003), 818-821.

[31] L. Zhou and D. M. Roche, An expression index for Affymetrix GeneChip based on the generalized logarithm, Biostatistics 21 (2005), 3983-3989.