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Microarray normalization and optimization

Edited by: Dr Leming Shi

Analyses of the increasing amount of data generated by the use of microarrays is a challenging task. In this topical series, we present a collection of technical notes and short reports on microarray standardization and optimization methods. From chip validation to improvement of data quality and analysis, the studies presented here tackle some of the most relevant issues in the post-genomic era.

Collection published: 19 August 2008

Last updated: 28 December 2010

		Research article Exploring the use of internal and externalcontrols for assessing microarray technical performance Katrice A Lippa, David L Duewer, Marc L Salit, Laurence Game, Helen C Causton BMC Research Notes 2010, 3:349 (28 December 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note EMA - A R package for Easy Microarray data analysis Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Isabel Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé BMC Research Notes 2010, 3:277 (3 November 2010) Abstract \| Full text \| PDF \| PubMed \| 1 comment
		Technical Note Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays Alexandra Schosser, Katrina Pirlo, Darya Gaysina, Sarah Cohen-Woods, Leonard C Schalkwyk, Amanda Elkin, Ania Korszun, Cerisse Gunasinghe, Joanna Gray, Lisa Jones, Emma Meaburn, Anne E Farmer, Ian W Craig, Peter McGuffin BMC Research Notes 2010, 3:274 (1 November 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours Stine H Kresse, Karoly Szuhai, Ana H Barragan-Polania, Halfdan Rydbeck, Anne-Marie Cleton-Jansen, Ola Myklebost, Leonardo A Meza-Zepeda BMC Research Notes 2010, 3:223 (8 August 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note RankProdIt: A web-interactive Rank Products analysis tool Emma Laing, Colin P Smith BMC Research Notes 2010, 3:221 (6 August 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example Han Rauwerda, Mark de Jong, Wim C de Leeuw, Herman P Spaink, Timo M Breit BMC Research Notes 2010, 3:192 (13 July 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina Frédérique Bidard, Sandrine Imbeaud, Nancie Reymond, Olivier Lespinet, Philippe Silar, Corinne Clavé, Hervé Delacroix, Véronique Berteaux-Lecellier, Robert Debuchy BMC Research Notes 2010, 3:171 (18 June 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome Leandro M Moreira, Marcelo L de Laia, Robson F de Souza, Paulo A Zaini, Ana CR da Silva, Aline M da Silva, Jesus A Ferro BMC Research Notes 2010, 3:150 (27 May 2010) Abstract \| Full text \| PDF \| PubMed
		Short Report Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays Colin S Gillespie, Guiyuan Lei, Richard J Boys, Amanda Greenall, Darren J Wilkinson BMC Research Notes 2010, 3:81 (19 March 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Performance evaluation of commercial miRNA expression array platforms Sachin Sah, Matthew N McCall, Deepa Eveleigh, Michael Wilson, Rafael A Irizarry BMC Research Notes 2010, 3:80 (18 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Short Report Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation Elizabeth A Tindall, Desiree C Petersen, Stina Nikolaysen, Webb Miller, Stephan C Schuster, Vanessa M Hayes BMC Research Notes 2010, 3:39 (22 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Short Report Processing of Agilent microRNA array data Pedro López-Romero, Manuel A González, Sergio Callejas, Ana Dopazo, Rafael A Irizarry BMC Research Notes 2010, 3:18 (22 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Technical Note Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays Jarmo Ritari, Lars Paulin, Jenni Hultman, Petri Auvinen BMC Research Notes 2009, 2:249 (14 December 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Use of per-spot hybridization control probes and a novel computing normalization technique improves the signal to noise ratio and reduces artefacts of diagnostic microarrays, so increasing the statistical significance of the data generated.
		Short Report Comparison of threshold selection methods for microarray gene co-expression matrices Bhavesh R Borate, Elissa J Chesler, Michael A Langston, Arnold M Saxton, Brynn H Voy BMC Research Notes 2009, 2:240 (2 December 2009) Abstract \| Full text \| PDF \| PubMed
		Short Report Advanced spot quality analysis in two-colour microarray experiments Mikalai Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich BMC Research Notes 2008, 1:80 (17 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Technical Note Salvaging Affymetrix probes after probe-level re-annotation Wim C de Leeuw, Han Rauwerda, Martijs J Jonker, Timo M Breit BMC Research Notes 2008, 1:66 (19 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Technical Note Development and application of a microarray meter tool to optimize microarray experiments Richard JD Rouse, Katrine Field, Jennifer Lapira, Allen Lee, Ivan Wick, Colleen Eckhardt, C Ramana Bhasker, Laura Soverchia, Gary Hardiman BMC Research Notes 2008, 1:45 (11 July 2008) Abstract \| Full text \| PDF \| PubMed
		Short Report Spike-in validation of an Illumina-specific variance-stabilizing transformation Mark J Dunning, Matthew E Ritchie, Nuno L Barbosa-Morais, Simon Tavaré, Andy G Lynch BMC Research Notes 2008, 1:18 (4 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central

		Research article Exploring the use of internal and externalcontrols for assessing microarray technical performance Katrice A Lippa, David L Duewer, Marc L Salit, Laurence Game, Helen C Causton BMC Research Notes 2010, 3:349 (28 December 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note EMA - A R package for Easy Microarray data analysis Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Isabel Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé BMC Research Notes 2010, 3:277 (3 November 2010) Abstract \| Full text \| PDF \| PubMed \| 1 comment
		Technical Note Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays Alexandra Schosser, Katrina Pirlo, Darya Gaysina, Sarah Cohen-Woods, Leonard C Schalkwyk, Amanda Elkin, Ania Korszun, Cerisse Gunasinghe, Joanna Gray, Lisa Jones, Emma Meaburn, Anne E Farmer, Ian W Craig, Peter McGuffin BMC Research Notes 2010, 3:274 (1 November 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours Stine H Kresse, Karoly Szuhai, Ana H Barragan-Polania, Halfdan Rydbeck, Anne-Marie Cleton-Jansen, Ola Myklebost, Leonardo A Meza-Zepeda BMC Research Notes 2010, 3:223 (8 August 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note RankProdIt: A web-interactive Rank Products analysis tool Emma Laing, Colin P Smith BMC Research Notes 2010, 3:221 (6 August 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example Han Rauwerda, Mark de Jong, Wim C de Leeuw, Herman P Spaink, Timo M Breit BMC Research Notes 2010, 3:192 (13 July 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina Frédérique Bidard, Sandrine Imbeaud, Nancie Reymond, Olivier Lespinet, Philippe Silar, Corinne Clavé, Hervé Delacroix, Véronique Berteaux-Lecellier, Robert Debuchy BMC Research Notes 2010, 3:171 (18 June 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome Leandro M Moreira, Marcelo L de Laia, Robson F de Souza, Paulo A Zaini, Ana CR da Silva, Aline M da Silva, Jesus A Ferro BMC Research Notes 2010, 3:150 (27 May 2010) Abstract \| Full text \| PDF \| PubMed
		Short Report Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays Colin S Gillespie, Guiyuan Lei, Richard J Boys, Amanda Greenall, Darren J Wilkinson BMC Research Notes 2010, 3:81 (19 March 2010) Abstract \| Full text \| PDF \| PubMed
		Technical Note Performance evaluation of commercial miRNA expression array platforms Sachin Sah, Matthew N McCall, Deepa Eveleigh, Michael Wilson, Rafael A Irizarry BMC Research Notes 2010, 3:80 (18 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Short Report Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation Elizabeth A Tindall, Desiree C Petersen, Stina Nikolaysen, Webb Miller, Stephan C Schuster, Vanessa M Hayes BMC Research Notes 2010, 3:39 (22 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Short Report Processing of Agilent microRNA array data Pedro López-Romero, Manuel A González, Sergio Callejas, Ana Dopazo, Rafael A Irizarry BMC Research Notes 2010, 3:18 (22 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Technical Note Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays Jarmo Ritari, Lars Paulin, Jenni Hultman, Petri Auvinen BMC Research Notes 2009, 2:249 (14 December 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Use of per-spot hybridization control probes and a novel computing normalization technique improves the signal to noise ratio and reduces artefacts of diagnostic microarrays, so increasing the statistical significance of the data generated.
		Short Report Comparison of threshold selection methods for microarray gene co-expression matrices Bhavesh R Borate, Elissa J Chesler, Michael A Langston, Arnold M Saxton, Brynn H Voy BMC Research Notes 2009, 2:240 (2 December 2009) Abstract \| Full text \| PDF \| PubMed
		Short Report Advanced spot quality analysis in two-colour microarray experiments Mikalai Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich BMC Research Notes 2008, 1:80 (17 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Technical Note Salvaging Affymetrix probes after probe-level re-annotation Wim C de Leeuw, Han Rauwerda, Martijs J Jonker, Timo M Breit BMC Research Notes 2008, 1:66 (19 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Technical Note Development and application of a microarray meter tool to optimize microarray experiments Richard JD Rouse, Katrine Field, Jennifer Lapira, Allen Lee, Ivan Wick, Colleen Eckhardt, C Ramana Bhasker, Laura Soverchia, Gary Hardiman BMC Research Notes 2008, 1:45 (11 July 2008) Abstract \| Full text \| PDF \| PubMed
		Short Report Spike-in validation of an Illumina-specific variance-stabilizing transformation Mark J Dunning, Matthew E Ritchie, Nuno L Barbosa-Morais, Simon Tavaré, Andy G Lynch BMC Research Notes 2008, 1:18 (4 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central