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Minimum Information About a Microarray Experiment - MIAME

Minimum Information About a Microarray Experiment - MIAME. MGED 5 workshop. Quantitation matrices. Gene expression data matrix. Raw data. Array scans. Quantitations. Samples. Spots. Genes. Gene expression levels. Which data to share?. Sample annotations. Gene expression levels.

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Minimum Information About a Microarray Experiment - MIAME

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  1. Minimum Information About a Microarray Experiment - MIAME MGED 5 workshop

  2. Quantitation matrices Gene expression data matrix Raw data Array scans Quantitations Samples Spots Genes Gene expression levels Which data to share?

  3. Sample annotations Gene expression levels Gene annotations Annotations Samples Gene expression matrix Genes

  4. source Sample Design treatment protocols RNA extract elements (spots) labelled nucleic acid array image quantitation matrix hybridisation Sample annotation Gene annotation

  5. Sample Sample Sample Sample Sample Design Design Design Design Design RNA extract RNA extract RNA extract RNA extract RNA extract elements (spots) elements (spots) elements (spots) elements (spots) elements (spots) labelled nucleic acid labelled nucleic acid labelled nucleic acid labelled nucleic acid labelled nucleic acid hybridisation hybridisation hybridisation hybridisation hybridisation array array array array array Gene expression data matrix transformation integration Experiment Gene expression measurements

  6. Sample Sample Sample Sample Sample Design Design Design Design Design RNA extract RNA extract RNA extract RNA extract RNA extract elements (spots) elements (spots) elements (spots) elements (spots) elements (spots) labelled nucleic acid labelled nucleic acid labelled nucleic acid labelled nucleic acid labelled nucleic acid hybridisation hybridisation hybridisation hybridisation hybridisation array array array array array Gene expression data matrix normalization integration Experiment MIAME – the content (annotation) of all boxes and lines should be given

  7. MIAME ‘checklist’ to authors and reviewers • Experimental design • Samples used, RNA extraction and labelling • Hybridisation • Measurement data and specifications • (Raw images) • Image quantitation (data and specification) • Gene expression data matrix (data and transformations) • Array design

  8. Nature and The Lancet is adopting compliance to MIAME checklist as a requirement for publishing microarray papers!

  9. Questions • Is MIAME a good or a bad idea? • Is everything what is included in MIAME really necessary for data sharing? • Is something missing? • How would you like MIAME to be changed? www.mged.org/miame

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