M. Ortiz-Estevez*, A. Aramburu*, H. Bengtsson*, P. Neuvial* & A. Rubio*, CalMaTe: A method and software to improve allele-specific copy number of SNP arrays for downstream segmentation, Bioinformatics, 2012.
[abstractPDF, Supplementary Material: 3 PDFs. PMID: 22576175]
Cite this for: CalMaTe

A.B. Olshen*, H. Bengtsson*, P. Neuvial, P. Spellman, R.A. Olshen, V.E. Seshan, Parent-specific copy number in paired tumor-normal studies using circular binary segmentation, Bioinformatics, 2011.
[abstractPDF, Supplementary Material: 1 PDF. PMID: 21666266]
Cite this for: Paired PSCBS

P. Neuvial, H. Bengtsson and T. P. Speed, Statistical analysis of Single Nucleotide Polymorphism microarrays in cancer studies, HHS Lu, B Schölkopf, H Zhao (Eds.), Handbook of Statistical Bioinformatics, Springer, 2011 (pp. 225--255).
[online preview, ISBN: 978-3-642-16344-9 (Print) 978-3-642-16345-6 (Online); preprint]

M. Ortiz-Estevez, H. Bengtsson, A. Rubio, ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays, Bioinformatics, 2010.
[abstract, PDF, Supplementary Material: 1 PDF. PMID: 20529889]
Cite this for: ACNE

H. Bengtsson*, P. Neuvial* & T.P. Speed, TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays, BMC Bioinformatics, 2010. (* equal contributions)
[abstract, PDF, Supplementary Materials: 12 PDFs, poster. PMID: 20462408]
Cite this for: TumorBoost, Paired PSCBS (since it uses TumorBoost)

H. Bengtsson, P. Wirapati & T.P. Speed, A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, Bioinformatics, 2009.
[abstract, PDF. Supplementary Materials: (1) PDF, (2) PDF, (3) PDF. PMID: 19535535]
Cite this for: CRMA v2 or any of its preprocessing components

M.D. Robinson & T.P. Speed. Differential splicing using whole-transcript microarrays, BMC Bioinformatics, 2009, 10, 156.
[abstract, PDF. Supplementary Materials: (1) PDF, (2) zip, (3) zip. PMID: 19463149]
Cite this for: FIRMAGene

H. Bengtsson, A. Ray, P. Spellman & T.P. Speed, A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods, Bioinformatics 2009.
[abstract, PDF. PMID: 19193730]
Cite this for: MSCN

H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics 2008, 24, pp759-767.
[abstract, PDF. Supplementary Materials: (1) PDF. PMID: 18204055]
Cite this for: CRMA (v1) or any of its preprocessing components, or estimate bias-corrected sex-chromosome copy numbers.

H. Bengtsson, K. Simpson, J. Bullard & K. Hansen, aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008.
[abstract, PDF]
Cite this for: aroma.affymetrix (or aroma.core or

E. Purdom, K. Simpson, M. Robinson, J. Conboy, A. Lapuk & T.P. Speed, FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics, 2008.
[abstract, PDF. Supplementary Materials: (1) PDF, (2) PDF, (3) PDF, (4) tab. PMID: 18573797]
Cite this for: FIRMA

M.D. Robinson & T.P. Speed. A comparison of Affymetrix gene expression arrays. BMC Bioinformatics, 2007, 8, 449.
[abstract, PDF. Supplementary Materials: (1) PDF. PMID: 18005448]

B. Carvalho, H. Bengtsson, T.P. Speed & R.A. Irizarry. Exploration, Normalization, and Genotype Calls of High Density Oligonucleotide SNP Array Data. Biostatistics, 2006.
[abstract, PDF. Supplementary Materials: 9 files. PMID: 17189563]
Cite this for: CRLMM

H. Bengtsson & O. Hössjer, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. BMC Bioinformatics, 2006
[abstractPDF. PMID: 16509971]
Cite this for: background/offset in signals, the affine normalization method and/or aroma.light or aroma.

A. Bengtsson & H. Bengtsson, Microarray image analysis: background estimation using quantile and morphological filters BMC Bioinformatics, 2006.
[abstractPDF. PMID: 16504173]
Cite this for: ...

H. Bengtsson, G. Jönsson & J. Vallon-Christersson. Calibration and assessment of channel-specific biases in microarray data with extended dynamical range, BMC Bioinformatics, 2004
[abstractPDF. PMID: 15541170]
Cite this for: the multiscan calibration method and/or aroma.light or aroma.

H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), 2003.
[abstract, PDF]
Cite this for: reference variables, object-oriented methods in R, R.methodsS3 or R.oo (for your development)

H Bengtsson, Identification and normalization of plate effects in cDNA microarray data, Preprints in Mathematical Statistics, Lund University, 2002.
[abstract, PDF]
Cite this for: discussion print-order and/or plate effects