The EADGENE Microarray Data Analysis Workshop (Open Access publication)
Identifieur interne : 000428 ( Pmc/Checkpoint ); précédent : 000427; suivant : 000429The EADGENE Microarray Data Analysis Workshop (Open Access publication)
Auteurs : Dirk-Jan De Koning [Royaume-Uni] ; Florence Jaffrézic [France] ; Mogens Sand Lund [Danemark] ; Michael Watson [Royaume-Uni] ; Caroline Channing [Royaume-Uni] ; Ina Hulsegge [Pays-Bas] ; Marco H. Pool [Pays-Bas] ; Bart Buitenhuis [Danemark] ; Jakob Hedegaard [Danemark] ; Henrik Hornsh J [Danemark] ; Li Jiang [Danemark] ; Peter S Rensen [Danemark] ; Guillemette Marot [France] ; Céline Delmas [France] ; Kim-Anh Lê Cao [France] ; Magali San Cristobal [France] ; Michael D. Baron [Royaume-Uni] ; Roberto Malinverni [Italie] ; Alessandra Stella [Italie] ; Ronald M. Brunner [Allemagne] ; Hans-Martin Seyfert [Allemagne] ; Kirsty Jensen [Royaume-Uni] ; Daphne Mouzaki [Royaume-Uni] ; David Waddington [Royaume-Uni] ; Ángeles Jiménez-Marín [Espagne] ; M Nica Pérez-Alegre [Espagne] ; Eva Pérez-Reinado [Espagne] ; Rodrigue Closset [Belgique] ; Johanne C. Detilleux [Royaume-Uni] ; Peter Dov [Slovénie] ; Miha Lavri [Slovénie] ; Haisheng Nie [Pays-Bas] ; Luc Janss [Danemark]Source :
- Genetics, Selection, Evolution : GSE [ 0999-193X ] ; 2007.
Abstract
Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.
Url:
DOI: 10.1186/1297-9686-39-6-621
PubMed: 18053572
PubMed Central: 2682810
Affiliations:
- Allemagne, Belgique, Danemark, Espagne, France, Italie, Pays-Bas, Royaume-Uni, Slovénie
- Midi-Pyrénées, Occitanie (région administrative)
- Toulouse
- Université Toulouse III - Paul Sabatier
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PMC:2682810Le document en format XML
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<author><name sortKey="Mouzaki, Daphne" sort="Mouzaki, Daphne" uniqKey="Mouzaki D" first="Daphne" last="Mouzaki">Daphne Mouzaki</name>
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<author><name sortKey="Jimenez Marin, Angeles" sort="Jimenez Marin, Angeles" uniqKey="Jimenez Marin A" first="Ángeles" last="Jiménez-Marín">Ángeles Jiménez-Marín</name>
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<author><name sortKey="Closset, Rodrigue" sort="Closset, Rodrigue" uniqKey="Closset R" first="Rodrigue" last="Closset">Rodrigue Closset</name>
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<author><name sortKey="Detilleux, Johanne C" sort="Detilleux, Johanne C" uniqKey="Detilleux J" first="Johanne C" last="Detilleux">Johanne C. Detilleux</name>
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<author><name sortKey="Dov, Peter" sort="Dov, Peter" uniqKey="Dov P" first="Peter" last="Dov">Peter Dov</name>
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<author><name sortKey="Nie, Haisheng" sort="Nie, Haisheng" uniqKey="Nie H" first="Haisheng" last="Nie">Haisheng Nie</name>
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<author><name sortKey="Janss, Luc" sort="Janss, Luc" uniqKey="Janss L" first="Luc" last="Janss">Luc Janss</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The EADGENE Microarray Data Analysis Workshop (<italic>Open Access publication</italic>
)</title>
<author><name sortKey="De Koning, Dirk Jan" sort="De Koning, Dirk Jan" uniqKey="De Koning D" first="Dirk-Jan" last="De Koning">Dirk-Jan De Koning</name>
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<author><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name>
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<author><name sortKey="Lund, Mogens Sand" sort="Lund, Mogens Sand" uniqKey="Lund M" first="Mogens Sand" last="Lund">Mogens Sand Lund</name>
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<country xml:lang="fr">Danemark</country>
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<author><name sortKey="Watson, Michael" sort="Watson, Michael" uniqKey="Watson M" first="Michael" last="Watson">Michael Watson</name>
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<author><name sortKey="Channing, Caroline" sort="Channing, Caroline" uniqKey="Channing C" first="Caroline" last="Channing">Caroline Channing</name>
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<author><name sortKey="Hulsegge, Ina" sort="Hulsegge, Ina" uniqKey="Hulsegge I" first="Ina" last="Hulsegge">Ina Hulsegge</name>
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<country xml:lang="fr">Pays-Bas</country>
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</author>
<author><name sortKey="Pool, Marco H" sort="Pool, Marco H" uniqKey="Pool M" first="Marco H" last="Pool">Marco H. Pool</name>
<affiliation wicri:level="1"><nlm:aff id="I5">Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Animal Sciences Group Wageningen UR, Lelystad</wicri:regionArea>
<wicri:noRegion>Lelystad</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Buitenhuis, Bart" sort="Buitenhuis, Bart" uniqKey="Buitenhuis B" first="Bart" last="Buitenhuis">Bart Buitenhuis</name>
<affiliation wicri:level="1"><nlm:aff id="I3">University of Aarhus, Tjele, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>University of Aarhus, Tjele</wicri:regionArea>
<wicri:noRegion>Tjele</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Hedegaard, Jakob" sort="Hedegaard, Jakob" uniqKey="Hedegaard J" first="Jakob" last="Hedegaard">Jakob Hedegaard</name>
<affiliation wicri:level="1"><nlm:aff id="I3">University of Aarhus, Tjele, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>University of Aarhus, Tjele</wicri:regionArea>
<wicri:noRegion>Tjele</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Hornsh J, Henrik" sort="Hornsh J, Henrik" uniqKey="Hornsh J H" first="Henrik" last="Hornsh J">Henrik Hornsh J</name>
<affiliation wicri:level="1"><nlm:aff id="I3">University of Aarhus, Tjele, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>University of Aarhus, Tjele</wicri:regionArea>
<wicri:noRegion>Tjele</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jiang, Li" sort="Jiang, Li" uniqKey="Jiang L" first="Li" last="Jiang">Li Jiang</name>
<affiliation wicri:level="1"><nlm:aff id="I3">University of Aarhus, Tjele, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>University of Aarhus, Tjele</wicri:regionArea>
<wicri:noRegion>Tjele</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="S Rensen, Peter" sort="S Rensen, Peter" uniqKey="S Rensen P" first="Peter" last="S Rensen">Peter S Rensen</name>
<affiliation wicri:level="1"><nlm:aff id="I3">University of Aarhus, Tjele, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>University of Aarhus, Tjele</wicri:regionArea>
<wicri:noRegion>Tjele</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Marot, Guillemette" sort="Marot, Guillemette" uniqKey="Marot G" first="Guillemette" last="Marot">Guillemette Marot</name>
<affiliation wicri:level="1"><nlm:aff id="I2">INRA, UR337, Jouy-en-Josas, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>INRA, UR337, Jouy-en-Josas</wicri:regionArea>
<wicri:noRegion>Jouy-en-Josas</wicri:noRegion>
<wicri:noRegion>Jouy-en-Josas</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Delmas, Celine" sort="Delmas, Celine" uniqKey="Delmas C" first="Céline" last="Delmas">Céline Delmas</name>
<affiliation wicri:level="1"><nlm:aff id="I6">INRA, UMR444, Castanet-Tolosan, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>INRA, UMR444, Castanet-Tolosan</wicri:regionArea>
<wicri:noRegion>Castanet-Tolosan</wicri:noRegion>
<wicri:noRegion>Castanet-Tolosan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cao, Kim Anh Le" sort="Cao, Kim Anh Le" uniqKey="Cao K" first="Kim-Anh Lê" last="Cao">Kim-Anh Lê Cao</name>
<affiliation wicri:level="1"><nlm:aff id="I6">INRA, UMR444, Castanet-Tolosan, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>INRA, UMR444, Castanet-Tolosan</wicri:regionArea>
<wicri:noRegion>Castanet-Tolosan</wicri:noRegion>
<wicri:noRegion>Castanet-Tolosan</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="I7">Université Paul Sabatier, Toulouse, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Université Paul Sabatier, Toulouse</wicri:regionArea>
<placeName><settlement type="city">Toulouse</settlement>
</placeName>
<orgName type="university">Université Toulouse III - Paul Sabatier</orgName>
<placeName><settlement type="city">Toulouse</settlement>
<region type="region" nuts="2">Occitanie (région administrative)</region>
<region type="old region" nuts="2">Midi-Pyrénées</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="San Cristobal, Magali" sort="San Cristobal, Magali" uniqKey="San Cristobal M" first="Magali" last="San Cristobal">Magali San Cristobal</name>
<affiliation wicri:level="1"><nlm:aff id="I6">INRA, UMR444, Castanet-Tolosan, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>INRA, UMR444, Castanet-Tolosan</wicri:regionArea>
<wicri:noRegion>Castanet-Tolosan</wicri:noRegion>
<wicri:noRegion>Castanet-Tolosan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Baron, Michael D" sort="Baron, Michael D" uniqKey="Baron M" first="Michael D" last="Baron">Michael D. Baron</name>
<affiliation wicri:level="1"><nlm:aff id="I8">Institute for Animal Health, Pirbright, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Institute for Animal Health, Pirbright</wicri:regionArea>
<wicri:noRegion>Pirbright</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Malinverni, Roberto" sort="Malinverni, Roberto" uniqKey="Malinverni R" first="Roberto" last="Malinverni">Roberto Malinverni</name>
<affiliation wicri:level="1"><nlm:aff id="I9">Parco Tecnologico Padano (PTP), Lodi, Italy</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Parco Tecnologico Padano (PTP), Lodi</wicri:regionArea>
<wicri:noRegion>Lodi</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Stella, Alessandra" sort="Stella, Alessandra" uniqKey="Stella A" first="Alessandra" last="Stella">Alessandra Stella</name>
<affiliation wicri:level="1"><nlm:aff id="I9">Parco Tecnologico Padano (PTP), Lodi, Italy</nlm:aff>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Parco Tecnologico Padano (PTP), Lodi</wicri:regionArea>
<wicri:noRegion>Lodi</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Brunner, Ronald M" sort="Brunner, Ronald M" uniqKey="Brunner R" first="Ronald M" last="Brunner">Ronald M. Brunner</name>
<affiliation wicri:level="1"><nlm:aff id="I10">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Research Institute for the Biology of Farm Animals, Dummerstorf</wicri:regionArea>
<wicri:noRegion>Dummerstorf</wicri:noRegion>
<wicri:noRegion>Dummerstorf</wicri:noRegion>
<wicri:noRegion>Dummerstorf</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Seyfert, Hans Martin" sort="Seyfert, Hans Martin" uniqKey="Seyfert H" first="Hans-Martin" last="Seyfert">Hans-Martin Seyfert</name>
<affiliation wicri:level="1"><nlm:aff id="I10">Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Research Institute for the Biology of Farm Animals, Dummerstorf</wicri:regionArea>
<wicri:noRegion>Dummerstorf</wicri:noRegion>
<wicri:noRegion>Dummerstorf</wicri:noRegion>
<wicri:noRegion>Dummerstorf</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jensen, Kirsty" sort="Jensen, Kirsty" uniqKey="Jensen K" first="Kirsty" last="Jensen">Kirsty Jensen</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Roslin Institute, Roslin, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Roslin Institute, Roslin</wicri:regionArea>
<wicri:noRegion>Roslin</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mouzaki, Daphne" sort="Mouzaki, Daphne" uniqKey="Mouzaki D" first="Daphne" last="Mouzaki">Daphne Mouzaki</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Roslin Institute, Roslin, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Roslin Institute, Roslin</wicri:regionArea>
<wicri:noRegion>Roslin</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Waddington, David" sort="Waddington, David" uniqKey="Waddington D" first="David" last="Waddington">David Waddington</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Roslin Institute, Roslin, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Roslin Institute, Roslin</wicri:regionArea>
<wicri:noRegion>Roslin</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jimenez Marin, Angeles" sort="Jimenez Marin, Angeles" uniqKey="Jimenez Marin A" first="Ángeles" last="Jiménez-Marín">Ángeles Jiménez-Marín</name>
<affiliation wicri:level="1"><nlm:aff id="I11">University of Córdoba, Córdoba, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>University of Córdoba, Córdoba</wicri:regionArea>
<wicri:noRegion>Córdoba</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Perez Alegre, M Nica" sort="Perez Alegre, M Nica" uniqKey="Perez Alegre M" first="M Nica" last="Pérez-Alegre">M Nica Pérez-Alegre</name>
<affiliation wicri:level="1"><nlm:aff id="I11">University of Córdoba, Córdoba, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>University of Córdoba, Córdoba</wicri:regionArea>
<wicri:noRegion>Córdoba</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Perez Reinado, Eva" sort="Perez Reinado, Eva" uniqKey="Perez Reinado E" first="Eva" last="Pérez-Reinado">Eva Pérez-Reinado</name>
<affiliation wicri:level="1"><nlm:aff id="I11">University of Córdoba, Córdoba, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>University of Córdoba, Córdoba</wicri:regionArea>
<wicri:noRegion>Córdoba</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Closset, Rodrigue" sort="Closset, Rodrigue" uniqKey="Closset R" first="Rodrigue" last="Closset">Rodrigue Closset</name>
<affiliation wicri:level="1"><nlm:aff id="I12">University of Liege, Liege, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>University of Liege, Liege</wicri:regionArea>
<wicri:noRegion>Liege</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Detilleux, Johanne C" sort="Detilleux, Johanne C" uniqKey="Detilleux J" first="Johanne C" last="Detilleux">Johanne C. Detilleux</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Roslin Institute, Roslin, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Roslin Institute, Roslin</wicri:regionArea>
<wicri:noRegion>Roslin</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Dov, Peter" sort="Dov, Peter" uniqKey="Dov P" first="Peter" last="Dov">Peter Dov</name>
<affiliation wicri:level="1"><nlm:aff id="I13">University of Ljubljana, Ljubljana, Slovenia</nlm:aff>
<country xml:lang="fr">Slovénie</country>
<wicri:regionArea>University of Ljubljana, Ljubljana</wicri:regionArea>
<wicri:noRegion>Ljubljana</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Lavri, Miha" sort="Lavri, Miha" uniqKey="Lavri M" first="Miha" last="Lavri">Miha Lavri</name>
<affiliation wicri:level="1"><nlm:aff id="I13">University of Ljubljana, Ljubljana, Slovenia</nlm:aff>
<country xml:lang="fr">Slovénie</country>
<wicri:regionArea>University of Ljubljana, Ljubljana</wicri:regionArea>
<wicri:noRegion>Ljubljana</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nie, Haisheng" sort="Nie, Haisheng" uniqKey="Nie H" first="Haisheng" last="Nie">Haisheng Nie</name>
<affiliation wicri:level="1"><nlm:aff id="I14">Wageningen University and Research Centre, Wageningen, The Netherlands</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Wageningen University and Research Centre, Wageningen</wicri:regionArea>
<wicri:noRegion>Wageningen</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Janss, Luc" sort="Janss, Luc" uniqKey="Janss L" first="Luc" last="Janss">Luc Janss</name>
<affiliation wicri:level="1"><nlm:aff id="I3">University of Aarhus, Tjele, Denmark</nlm:aff>
<country xml:lang="fr">Danemark</country>
<wicri:regionArea>University of Aarhus, Tjele</wicri:regionArea>
<wicri:noRegion>Tjele</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Genetics, Selection, Evolution : GSE</title>
<idno type="ISSN">0999-193X</idno>
<idno type="eISSN">1297-9686</idno>
<imprint><date when="2007">2007</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genet Sel Evol</journal-id>
<journal-title>Genetics, Selection, Evolution : GSE</journal-title>
<issn pub-type="ppub">0999-193X</issn>
<issn pub-type="epub">1297-9686</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">18053572</article-id>
<article-id pub-id-type="pmc">2682810</article-id>
<article-id pub-id-type="publisher-id">1297-9686-39-6-621</article-id>
<article-id pub-id-type="doi">10.1186/1297-9686-39-6-621</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research</subject>
</subj-group>
</article-categories>
<title-group><article-title>The EADGENE Microarray Data Analysis Workshop (<italic>Open Access publication</italic>
)</article-title>
</title-group>
<contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>de Koning</surname>
<given-names>Dirk-Jan</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>DJ.dekoning@bbsrc.ac.uk</email>
</contrib>
<contrib id="A2" contrib-type="author"><name><surname>Jaffrézic</surname>
<given-names>Florence</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Lund</surname>
<given-names>Mogens Sandø</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
</contrib>
<contrib id="A4" contrib-type="author"><name><surname>Watson</surname>
<given-names>Michael</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
</contrib>
<contrib id="A5" contrib-type="author"><name><surname>Channing</surname>
<given-names>Caroline</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
</contrib>
<contrib id="A6" contrib-type="author"><name><surname>Hulsegge</surname>
<given-names>Ina</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
</contrib>
<contrib id="A7" contrib-type="author"><name><surname>Pool</surname>
<given-names>Marco H</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
</contrib>
<contrib id="A8" contrib-type="author"><name><surname>Buitenhuis</surname>
<given-names>Bart</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
</contrib>
<contrib id="A9" contrib-type="author"><name><surname>Hedegaard</surname>
<given-names>Jakob</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
</contrib>
<contrib id="A10" contrib-type="author"><name><surname>Hornshøj</surname>
<given-names>Henrik</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
</contrib>
<contrib id="A11" contrib-type="author"><name><surname>Jiang</surname>
<given-names>Li</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
</contrib>
<contrib id="A12" contrib-type="author"><name><surname>Sørensen</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
</contrib>
<contrib id="A13" contrib-type="author"><name><surname>Marot</surname>
<given-names>Guillemette</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
</contrib>
<contrib id="A14" contrib-type="author"><name><surname>Delmas</surname>
<given-names>Céline</given-names>
</name>
<xref ref-type="aff" rid="I6">6</xref>
</contrib>
<contrib id="A15" contrib-type="author"><name><surname>Cao</surname>
<given-names>Kim-Anh Lê</given-names>
</name>
<xref ref-type="aff" rid="I6">6</xref>
<xref ref-type="aff" rid="I7">7</xref>
</contrib>
<contrib id="A16" contrib-type="author"><name><surname>San Cristobal</surname>
<given-names>Magali</given-names>
</name>
<xref ref-type="aff" rid="I6">6</xref>
</contrib>
<contrib id="A17" contrib-type="author"><name><surname>Baron</surname>
<given-names>Michael D</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
</contrib>
<contrib id="A18" contrib-type="author"><name><surname>Malinverni</surname>
<given-names>Roberto</given-names>
</name>
<xref ref-type="aff" rid="I9">9</xref>
</contrib>
<contrib id="A19" contrib-type="author"><name><surname>Stella</surname>
<given-names>Alessandra</given-names>
</name>
<xref ref-type="aff" rid="I9">9</xref>
</contrib>
<contrib id="A20" contrib-type="author"><name><surname>Brunner</surname>
<given-names>Ronald M</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
</contrib>
<contrib id="A21" contrib-type="author"><name><surname>Seyfert</surname>
<given-names>Hans-Martin</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
</contrib>
<contrib id="A22" contrib-type="author"><name><surname>Jensen</surname>
<given-names>Kirsty</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
</contrib>
<contrib id="A23" contrib-type="author"><name><surname>Mouzaki</surname>
<given-names>Daphne</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
</contrib>
<contrib id="A24" contrib-type="author"><name><surname>Waddington</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
</contrib>
<contrib id="A25" contrib-type="author"><name><surname>Jiménez-Marín</surname>
<given-names>Ángeles</given-names>
</name>
<xref ref-type="aff" rid="I11">11</xref>
</contrib>
<contrib id="A26" contrib-type="author"><name><surname>Pérez-Alegre</surname>
<given-names>Mónica</given-names>
</name>
<xref ref-type="aff" rid="I11">11</xref>
</contrib>
<contrib id="A27" contrib-type="author"><name><surname>Pérez-Reinado</surname>
<given-names>Eva</given-names>
</name>
<xref ref-type="aff" rid="I11">11</xref>
</contrib>
<contrib id="A28" contrib-type="author"><name><surname>Closset</surname>
<given-names>Rodrigue</given-names>
</name>
<xref ref-type="aff" rid="I12">12</xref>
</contrib>
<contrib id="A29" contrib-type="author"><name><surname>Detilleux</surname>
<given-names>Johanne C</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
</contrib>
<contrib id="A30" contrib-type="author"><name><surname>Dovč</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="I13">13</xref>
</contrib>
<contrib id="A31" contrib-type="author"><name><surname>Lavrič</surname>
<given-names>Miha</given-names>
</name>
<xref ref-type="aff" rid="I13">13</xref>
</contrib>
<contrib id="A32" contrib-type="author"><name><surname>Nie</surname>
<given-names>Haisheng</given-names>
</name>
<xref ref-type="aff" rid="I14">14</xref>
</contrib>
<contrib id="A33" contrib-type="author"><name><surname>Janss</surname>
<given-names>Luc</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Roslin Institute, Roslin, UK</aff>
<aff id="I2"><label>2</label>
INRA, UR337, Jouy-en-Josas, France</aff>
<aff id="I3"><label>3</label>
University of Aarhus, Tjele, Denmark</aff>
<aff id="I4"><label>4</label>
Institute for Animal Health, Compton, UK</aff>
<aff id="I5"><label>5</label>
Animal Sciences Group Wageningen UR, Lelystad, The Netherlands</aff>
<aff id="I6"><label>6</label>
INRA, UMR444, Castanet-Tolosan, France</aff>
<aff id="I7"><label>7</label>
Université Paul Sabatier, Toulouse, France</aff>
<aff id="I8"><label>8</label>
Institute for Animal Health, Pirbright, UK</aff>
<aff id="I9"><label>9</label>
Parco Tecnologico Padano (PTP), Lodi, Italy</aff>
<aff id="I10"><label>10</label>
Research Institute for the Biology of Farm Animals, Dummerstorf, Germany</aff>
<aff id="I11"><label>11</label>
University of Córdoba, Córdoba, Spain</aff>
<aff id="I12"><label>12</label>
University of Liege, Liege, Belgium</aff>
<aff id="I13"><label>13</label>
University of Ljubljana, Ljubljana, Slovenia</aff>
<aff id="I14"><label>14</label>
Wageningen University and Research Centre, Wageningen, The Netherlands</aff>
<pub-date pub-type="collection"><year>2007</year>
</pub-date>
<pub-date pub-type="epub"><day>15</day>
<month>11</month>
<year>2007</year>
</pub-date>
<volume>39</volume>
<issue>6</issue>
<fpage>621</fpage>
<lpage>631</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.gse-journal.org/content/39/6/621"></ext-link>
<history><date date-type="received"><day>10</day>
<month>5</month>
<year>2007</year>
</date>
<date date-type="accepted"><day>3</day>
<month>7</month>
<year>2007</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2007 INRA, EDP Sciences</copyright-statement>
<copyright-year>2007</copyright-year>
<copyright-holder>INRA, EDP Sciences</copyright-holder>
</permissions>
<abstract><p>Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.</p>
</abstract>
<kwd-group><kwd>gene expression</kwd>
<kwd>two colour microarray</kwd>
<kwd>statistical analysis</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Allemagne</li>
<li>Belgique</li>
<li>Danemark</li>
<li>Espagne</li>
<li>France</li>
<li>Italie</li>
<li>Pays-Bas</li>
<li>Royaume-Uni</li>
<li>Slovénie</li>
</country>
<region><li>Midi-Pyrénées</li>
<li>Occitanie (région administrative)</li>
</region>
<settlement><li>Toulouse</li>
</settlement>
<orgName><li>Université Toulouse III - Paul Sabatier</li>
</orgName>
</list>
<tree><country name="Royaume-Uni"><noRegion><name sortKey="De Koning, Dirk Jan" sort="De Koning, Dirk Jan" uniqKey="De Koning D" first="Dirk-Jan" last="De Koning">Dirk-Jan De Koning</name>
</noRegion>
<name sortKey="Baron, Michael D" sort="Baron, Michael D" uniqKey="Baron M" first="Michael D" last="Baron">Michael D. Baron</name>
<name sortKey="Channing, Caroline" sort="Channing, Caroline" uniqKey="Channing C" first="Caroline" last="Channing">Caroline Channing</name>
<name sortKey="Detilleux, Johanne C" sort="Detilleux, Johanne C" uniqKey="Detilleux J" first="Johanne C" last="Detilleux">Johanne C. Detilleux</name>
<name sortKey="Jensen, Kirsty" sort="Jensen, Kirsty" uniqKey="Jensen K" first="Kirsty" last="Jensen">Kirsty Jensen</name>
<name sortKey="Mouzaki, Daphne" sort="Mouzaki, Daphne" uniqKey="Mouzaki D" first="Daphne" last="Mouzaki">Daphne Mouzaki</name>
<name sortKey="Waddington, David" sort="Waddington, David" uniqKey="Waddington D" first="David" last="Waddington">David Waddington</name>
<name sortKey="Watson, Michael" sort="Watson, Michael" uniqKey="Watson M" first="Michael" last="Watson">Michael Watson</name>
</country>
<country name="France"><noRegion><name sortKey="Jaffrezic, Florence" sort="Jaffrezic, Florence" uniqKey="Jaffrezic F" first="Florence" last="Jaffrézic">Florence Jaffrézic</name>
</noRegion>
<name sortKey="Cao, Kim Anh Le" sort="Cao, Kim Anh Le" uniqKey="Cao K" first="Kim-Anh Lê" last="Cao">Kim-Anh Lê Cao</name>
<name sortKey="Cao, Kim Anh Le" sort="Cao, Kim Anh Le" uniqKey="Cao K" first="Kim-Anh Lê" last="Cao">Kim-Anh Lê Cao</name>
<name sortKey="Delmas, Celine" sort="Delmas, Celine" uniqKey="Delmas C" first="Céline" last="Delmas">Céline Delmas</name>
<name sortKey="Marot, Guillemette" sort="Marot, Guillemette" uniqKey="Marot G" first="Guillemette" last="Marot">Guillemette Marot</name>
<name sortKey="San Cristobal, Magali" sort="San Cristobal, Magali" uniqKey="San Cristobal M" first="Magali" last="San Cristobal">Magali San Cristobal</name>
</country>
<country name="Danemark"><noRegion><name sortKey="Lund, Mogens Sand" sort="Lund, Mogens Sand" uniqKey="Lund M" first="Mogens Sand" last="Lund">Mogens Sand Lund</name>
</noRegion>
<name sortKey="Buitenhuis, Bart" sort="Buitenhuis, Bart" uniqKey="Buitenhuis B" first="Bart" last="Buitenhuis">Bart Buitenhuis</name>
<name sortKey="Hedegaard, Jakob" sort="Hedegaard, Jakob" uniqKey="Hedegaard J" first="Jakob" last="Hedegaard">Jakob Hedegaard</name>
<name sortKey="Hornsh J, Henrik" sort="Hornsh J, Henrik" uniqKey="Hornsh J H" first="Henrik" last="Hornsh J">Henrik Hornsh J</name>
<name sortKey="Janss, Luc" sort="Janss, Luc" uniqKey="Janss L" first="Luc" last="Janss">Luc Janss</name>
<name sortKey="Jiang, Li" sort="Jiang, Li" uniqKey="Jiang L" first="Li" last="Jiang">Li Jiang</name>
<name sortKey="S Rensen, Peter" sort="S Rensen, Peter" uniqKey="S Rensen P" first="Peter" last="S Rensen">Peter S Rensen</name>
</country>
<country name="Pays-Bas"><noRegion><name sortKey="Hulsegge, Ina" sort="Hulsegge, Ina" uniqKey="Hulsegge I" first="Ina" last="Hulsegge">Ina Hulsegge</name>
</noRegion>
<name sortKey="Nie, Haisheng" sort="Nie, Haisheng" uniqKey="Nie H" first="Haisheng" last="Nie">Haisheng Nie</name>
<name sortKey="Pool, Marco H" sort="Pool, Marco H" uniqKey="Pool M" first="Marco H" last="Pool">Marco H. Pool</name>
</country>
<country name="Italie"><noRegion><name sortKey="Malinverni, Roberto" sort="Malinverni, Roberto" uniqKey="Malinverni R" first="Roberto" last="Malinverni">Roberto Malinverni</name>
</noRegion>
<name sortKey="Stella, Alessandra" sort="Stella, Alessandra" uniqKey="Stella A" first="Alessandra" last="Stella">Alessandra Stella</name>
</country>
<country name="Allemagne"><noRegion><name sortKey="Brunner, Ronald M" sort="Brunner, Ronald M" uniqKey="Brunner R" first="Ronald M" last="Brunner">Ronald M. Brunner</name>
</noRegion>
<name sortKey="Seyfert, Hans Martin" sort="Seyfert, Hans Martin" uniqKey="Seyfert H" first="Hans-Martin" last="Seyfert">Hans-Martin Seyfert</name>
</country>
<country name="Espagne"><noRegion><name sortKey="Jimenez Marin, Angeles" sort="Jimenez Marin, Angeles" uniqKey="Jimenez Marin A" first="Ángeles" last="Jiménez-Marín">Ángeles Jiménez-Marín</name>
</noRegion>
<name sortKey="Perez Alegre, M Nica" sort="Perez Alegre, M Nica" uniqKey="Perez Alegre M" first="M Nica" last="Pérez-Alegre">M Nica Pérez-Alegre</name>
<name sortKey="Perez Reinado, Eva" sort="Perez Reinado, Eva" uniqKey="Perez Reinado E" first="Eva" last="Pérez-Reinado">Eva Pérez-Reinado</name>
</country>
<country name="Belgique"><noRegion><name sortKey="Closset, Rodrigue" sort="Closset, Rodrigue" uniqKey="Closset R" first="Rodrigue" last="Closset">Rodrigue Closset</name>
</noRegion>
</country>
<country name="Slovénie"><noRegion><name sortKey="Dov, Peter" sort="Dov, Peter" uniqKey="Dov P" first="Peter" last="Dov">Peter Dov</name>
</noRegion>
<name sortKey="Lavri, Miha" sort="Lavri, Miha" uniqKey="Lavri M" first="Miha" last="Lavri">Miha Lavri</name>
</country>
</tree>
</affiliations>
</record>
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