quality control of thousands of experiments with qcml
DESCRIPTION
quality control of thousands of experiments with qcML. p ieter kelchtermans p ieter.kelchtermans @vib-ugent.be computational omics and systems biology group VIB / Ghent University, Ghent, Belgium. How do you want to do quality control What we tried to look at and how we did it - PowerPoint PPT PresentationTRANSCRIPT
quality control of thousands of experiments with qcML
pieter kelchtermans
[email protected] omics and systems biology groupVIB / Ghent University, Ghent, Belgium
How do you want to do quality control
What we tried to look at and how we did it
What we're looking forward to
We automated OpenMS
Process 5098 raw files to output qcML
Using Mathias Walzer’s workflow
Completely automated, on 11 linux computers
Preliminary analysis shows
You choose how to control the quality
qcML is a universal format
Captures metrics and metadata about all kinds of experiments
Separate from the actual analysis, only a container
Metrics are added with controlled vocabulary
qcML offers fast and easy access
QCExporter/QCExtractor gets data in tabular format
Java library under development by Wout Bittremieux
R integration with library by Laurent Gatto
Metrics can be generated by OpenMS
QuaMeter
Simpatiqco
You
Large-scale is not intractable
Automated deployment of virtual machines
OpenMS updates/installationConfigurationBatch data processing
Shared folder between all computers?
Be the master of your puppets
http://www.puppetlabs.com/ since 2005
Open source, cross platform agent
package { “openms”: ensure => "installed"}file { “/etc/openms.ini”: source => “puppet:///modules/openms/openms.ini“}
Each kind of experiment has different quality thresholds
Experiments vary a lot
Classification between experiments
Boundaries need to be determined by large-scale analysis
qcML allows for thresholds: flag bad experiments
Ratio of +1/+2 charged features
Ratio of +3/+2 charged features
Mean precursor m/z
900
600
Total Ion Current jumps
4000
1000
2000
3000
We’re shipping by the end of this year
Format definition: http://code.google.com/p/qcml/
Advanced analyses on differences between runs
Get in touch!
www.compomics.com@compomics
Wout BittremieuxMathias WalzerJonathan Vandenbussche, Kris Gevaert lab