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Microarray normalization and optimization

Analyses of the increasing amount of data generated by the use of microarrays is a challenging task. In this topical series, we presented 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.

Dr Leming Shi

  1. The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscri...

    Authors: Katrice A Lippa, David L Duewer, Marc L Salit, Laurence Game and Helen C Causton
    Citation: BMC Research Notes 2010 3:349
  2. The increasing number of methodologies and tools currently available to analyse gene expression microarray data can be confusing for non specialist users.

    Authors: Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Isabel Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot and Philippe Hupé
    Citation: BMC Research Notes 2010 3:277
  3. We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism) microarrays and DNA pooling (SNP-MaP) employing high-density microarrays. Whereas earlier stu...

    Authors: 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 and Peter McGuffin
    Citation: BMC Research Notes 2010 3:274
  4. Several high-density oligonucleotide microarray platforms are available for genome-wide single nucleotide polymorphism (SNP) detection and microarray-based comparative genomic hybridisation (array CGH), which ...

    Authors: Stine H Kresse, Karoly Szuhai, Ana H Barragan-Polania, Halfdan Rydbeck, Anne-Marie Cleton-Jansen, Ola Myklebost and Leonardo A Meza-Zepeda
    Citation: BMC Research Notes 2010 3:223
  5. The first objective of a DNA microarray experiment is typically to generate a list of genes or probes that are found to be differentially expressed or represented (in the case of comparative genomic hybridizat...

    Authors: Emma Laing and Colin P Smith
    Citation: BMC Research Notes 2010 3:221
  6. A complete gene-expression microarray should preferably detect all genomic sequences that can be expressed as RNA in an organism, i.e. the transcriptome. However, our knowledge of a transcriptome of any organi...

    Authors: Han Rauwerda, Mark de Jong, Wim C de Leeuw, Herman P Spaink and Timo M Breit
    Citation: BMC Research Notes 2010 3:192
  7. The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design ...

    Authors: Frédérique Bidard, Sandrine Imbeaud, Nancie Reymond, Olivier Lespinet, Philippe Silar, Corinne Clavé, Hervé Delacroix, Véronique Berteaux-Lecellier and Robert Debuchy
    Citation: BMC Research Notes 2010 3:171
  8. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (...

    Authors: Leandro M Moreira, Marcelo L de Laia, Robson F de Souza, Paulo A Zaini, Ana CR da Silva, Aline M da Silva and Jesus A Ferro
    Citation: BMC Research Notes 2010 3:150
  9. Large scale microarray experiments are becoming increasingly routine, particularly those which track a number of different cell lines through time. This time-course information provides valuable insight into t...

    Authors: Colin S Gillespie, Guiyuan Lei, Richard J Boys, Amanda Greenall and Darren J Wilkinson
    Citation: BMC Research Notes 2010 3:81
  10. microRNAs (miRNA) are short, endogenous transcripts that negatively regulate the expression of specific mRNA targets. The relative abundance of miRNAs is linked to function in vivo and miRNA expression patterns a...

    Authors: Sachin Sah, Matthew N McCall, Deepa Eveleigh, Michael Wilson and Rafael A Irizarry
    Citation: BMC Research Notes 2010 3:80
  11. High-throughput custom designed genotyping arrays are a valuable resource for biologically focused research studies and increasingly for validation of variation predicted by next-generation sequencing (NGS) te...

    Authors: Elizabeth A Tindall, Desiree C Petersen, Stina Nikolaysen, Webb Miller, Stephan C Schuster and Vanessa M Hayes
    Citation: BMC Research Notes 2010 3:39
  12. The Agilent microRNA microarray platform interrogates each microRNA with several copies of distinct oligonucleotide probes and integrates the results into a total gene signal (TGS), using a proprietary algorit...

    Authors: Pedro López-Romero, Manuel A González, Sergio Callejas, Ana Dopazo and Rafael A Irizarry
    Citation: BMC Research Notes 2010 3:18
  13. Nucleic acid detection based on ligation reaction or single nucleotide extension of ssDNA probes followed by tag microarray hybridization provides an accurate and sensitive detection tool for various diagnosti...

    Authors: Jarmo Ritari, Lars Paulin, Jenni Hultman and Petri Auvinen
    Citation: BMC Research Notes 2009 2:249
  14. Network and clustering analyses of microarray co-expression correlation data often require application of a threshold to discard small correlations, thus reducing computational demands and decreasing the numbe...

    Authors: Bhavesh R Borate, Elissa J Chesler, Michael A Langston, Arnold M Saxton and Brynn H Voy
    Citation: BMC Research Notes 2009 2:240
  15. Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality con...

    Authors: Mikalai Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar and Evelyne Friederich
    Citation: BMC Research Notes 2008 1:80
  16. Affymetrix GeneChips can be re-annotated at the probe-level by breaking up the original probe-sets and recomposing new probe-sets based on up-to-date genomic knowledge, such as available in Entrez Gene. This r...

    Authors: Wim C de Leeuw, Han Rauwerda, Martijs J Jonker and Timo M Breit
    Citation: BMC Research Notes 2008 1:66
  17. Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these param...

    Authors: Richard JD Rouse, Katrine Field, Jennifer Lapira, Allen Lee, Ivan Wick, Colleen Eckhardt, C Ramana Bhasker, Laura Soverchia and Gary Hardiman
    Citation: BMC Research Notes 2008 1:45
  18. Variance-stabilizing techniques have been used for some time in the analysis of gene expression microarray data. A new adaptation, the variance-stabilizing transformation (VST), has recently been developed to ...

    Authors: Mark J Dunning, Matthew E Ritchie, Nuno L Barbosa-Morais, Simon Tavaré and Andy G Lynch
    Citation: BMC Research Notes 2008 1:18