minimum information about a microarray experiment - miame mged 5 workshop
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Minimum Information About a Microarray Experiment
- MIAME
MGED 5 workshop
Raw data
Array scans
Spo
ts
Quantitations
Quantitationmatrices
Gen
es
Samples
Gene expressiondata matrix
Gene expression levels
Which data to share?
SamplesG
enes
Gene expression levels
Sample annotations
Gene annotations
Gene expression matrix
Annotations
hybridisationlabelled
nucleic acidarray
RNA extract
source
Sample treatment
elements(spots)
Design
protocols
image
quantitationmatrix
Sample annotation
Gene annotation
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
Experiment
Gene expression data matrix
transformation
integration
Gene expression measurements
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
hybridisationlabelled
nucleic acidarray
RNA extract
Sample
elements(spots)
Design
Experiment
Gene expression data matrix
normalization
integration
MIAME – the content (annotation) of all boxes and lines should be given
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
Nature and The Lancet is adopting compliance to MIAME
checklist as a requirement for publishing microarray papers!
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