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[1] M. Ortiz-Estevez, A. Aramburu, H. Bengtsson, et al. “CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation”. Eng. In: Bioinformatics (Oxford, England) 28.13 (Jul. 2012), pp. 1793-4. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/bts248. PMID: 22576175.
Keywords: CalMaTe; multi-array method

[2] P. Neuvial, H. Bengtsson, and T. P. Speed. “Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies”. In: Handbook of Statistical Bioinformatics. Springer Berlin Heidelberg, 2011, pp. 225-255. DOI: 10.1007/978-3-642-16345-6_11. URL:

[3] A. B. Olshen, H. Bengtsson, P. Neuvial, et al. “Parent-specific copy number in paired tumor-normal studies using circular binary segmentation”. Eng. In: Bioinformatics (Oxford, England) 27.15 (Aug. 2011), pp. 2038-46. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btr329. PMID: 21666266.
Keywords: PSCBS; parent-specific copy numbers; segmentation; tumor-normal samples; paired; non-paired; single-patient method

[4] H. Bengtsson, P. Neuvial, and T. P. Speed. “TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays”. Eng. In: BMC bioinformatics 11 (May. 2010), p. 245. ISSN: 1471-2105. DOI: 10.1186/1471-2105-11-245. PMID: 20462408.
Keywords: TumorBoost; paired tumor-normal samples; single-patient method

[5] M. Ortiz-Estevez, H. Bengtsson, and A. Rubio. “ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays”. Eng. In: Bioinformatics (Oxford, England) 26.15 (Aug. 2010), pp. 1827-33. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btq300. PMID: 20529889.
Keywords: ACNE; multi-array method

[6] H. Bengtsson, A. Ray, P. Spellman, et al. “A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods”. Eng. In: Bioinformatics (Oxford, England) 25.7 (Apr. 2009), pp. 861-7. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btp074. PMID: 19193730.
Keywords: MSCN; multi-source copy-number normalization; single-patient method

[7] [1] H. Bengtsson, P. Wirapati, and T. P. Speed. “A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6”. Eng. In: Bioinformatics (Oxford, England) 25.17 (Sep. 2009), pp. 2149-56. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btp371. PMID: 19535535.
Keywords: CRMA v2; single-array method

[8] M. D. Robinson and T. P. Speed. “Differential splicing using whole-transcript microarrays”. Eng. In: BMC bioinformatics 10 (May. 2009), p. 156. ISSN: 1471-2105. DOI: 10.1186/1471-2105-10-156. PMID: 19463149.
Keywords: FIRMAGene; multi-array method

[9] H. Bengtsson, R. Irizarry, B. Carvalho, et al. “Estimation and assessment of raw copy numbers at the single locus level”. Eng. In: Bioinformatics (Oxford, England) 24.6 (Mar. 2008), pp. 759-67. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btn016. PMID: 18204055.
Keywords: CRMA v1; multi-array method

[10] H. Bengtsson, K. Simpson, J. Bullard, et al. aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory. Tech. rep. 745. Department of Statistics, University of California, Berkeley, Feb. 2008.
Keywords: aroma.affymetrix; preprocessing; normalization; quality control; background correction; probe-sequence normalization; quantile normalization; probeset summarization

[11] E. Purdom, K. M. Simpson, M. D. Robinson, et al. “FIRMA: a method for detection of alternative splicing from exon array data”. Eng. In: Bioinformatics (Oxford, England) 24.15 (Aug. 2008), pp. 1707-14. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btn284. PMID: 18573797.
Keywords: FIRMA; gene expressions; exon-specific expressions; multi-array method

[12] B. Carvalho, H. Bengtsson, T. P. Speed, et al. “Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data”. Eng. In: Biostatistics (Oxford, England) 8.2 (Apr. 2007), pp. 485-99. ISSN: 1465-4644. DOI: 10.1093/biostatistics/kxl042. PMID: 17189563.
Keywords: CRLMM; genotyping; multi-array method

[13] M. D. Robinson and T. P. Speed. “A comparison of Affymetrix gene expression arrays”. Eng. In: BMC bioinformatics 8 (Nov. 2007), p. 449. ISSN: 1471-2105. DOI: 10.1186/1471-2105-8-449. PMID: 18005448.

[14] A. Bengtsson and H. Bengtsson. “Microarray image analysis: background estimation using quantile and morphological filters”. Eng. In: BMC bioinformatics 7 (Feb. 2006), p. 96. ISSN: 1471-2105. DOI: 10.1186/1471-2105-7-96. PMID: 16504173.
Keywords: image analysis; background correction; single-array method

[15] H. Bengtsson and O. Hössjer. “Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method”. Eng. In: BMC bioinformatics 7 (Mar. 2006), p. 100. ISSN: 1471-2105. DOI: 10.1186/1471-2105-7-100. PMID: 16509971.
Keywords: affine normalization; single-array method

[16] H. Bengtsson, G. Jönsson, and J. Vallon-Christersson. “Calibration and assessment of channel-specific biases in microarray data with extended dynamical range”. Eng. In: BMC bioinformatics 5 (Nov. 2004), p. 177. ISSN: 1471-2105. DOI: 10.1186/1471-2105-5-177. PMID: 15541170.
Keywords: multiscan calibration; single-array method

[17] H. Bengtsson. “The R.oo package - Object-Oriented Programming with References Using Standard R Code”. In: Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003). Ed. by K. Hornik, F. Leisch and A. Zeileis. Vienna, Austria, 2003. URL:
Keywords: R.methodsS3; R.oo; S3

[18] H. Bengtsson. Identification and normalization of plate effects in cDNA microarray data. Preprints in Mathematical Sciences 2002:28. MatStatLU, 2002.
Keywords: print-tip normalization; print-order effects; plate-order effects