NIH: Principles and Guidelines for Reporting Research
Rigorous statistical analysis
Transparency in reporting
Data & material sharing
Best practices
Interpretable statistical analysis
Effect size and significance
“EFFECT SIZE vs. SIGNIFICANCE: smoking increases your relative risk of lung cancer by 2,500 percent; eating two slices of bacon a day increases your relative risk for colorectal cancer by 18 percent. Given the frequency of colorectal cancer, that means your risk of getting colorectal cancer over your life goes from about 5 percent to 6 percent”
Interpretable statistical analysis
Multiple hypothesis testing
“Either we have stumbled onto a rather amazing discovery in terms of post-mortem ichthyological cognition, or there is something a bit off with regard to our uncorrected statistical approach.”
Craig M. Bennett, et al (2010). Neural Correlates of Interspecies Perspective Taking in the Post-Mortem Atlantic Salmon: An Argument For Proper Multiple Comparisons Correction Journal of Serendipitous and Unexpected Results, 1 (1), 1-5
Transparency in reporting
Standards
Replicates
Statistics
Randomizations
Blinding
Inclusion & exclusion criteria
Transparency in reporting
Standards
Replicates
Statistics
Randomizations
Blinding
Inclusion & exclusion criteria
MIAME (2001)
Minimum Information About a Microarray Experiment
Experimental conditions
Controlled vocabularies for organisms, gene functions
MIAME (2001)
A journal enforced reporting standard enables:
Reproducibility
Compare data
Compare method effectiveness
Refutability
Some more standards
Standard Purpose
Gene Ontology Protein function
Human Phenotype Ontology Human disease
MIxS Genomic and Metagenomic data
The Gene Ontology
Pingzhao Hu, Gary Bader, Dennis A. Wigle & Andrew Emili
Nature Reviews Cancer 7, 23-34 (January 2007)
The Gene Ontology
Consistent descriptions of genes
Mostly Human, mouse, fly & yeast
Functional aspects:
Molecular function
Biological process
Cellular component
Shape of Things
Useful standards & best practices exist in many fields
Funders beginning to understand needs for standards / best practices
Support for cyberinfrastructure
Education / awareness
Journal-mandated compliance
Funder based compliance(?)
Good Could be better