EMERALD

EMERALD Micoarray Quality Newsletter Nr.4 available

26 January 2010

The forth issue of the EMERALD Microarray Quality Newsletter is now available and can be downloaded here.

To subscribe for furure issues, please fill in the form above at this page.

 

 

EMERALD session in conjugation the 6th annual Integrative Bioinformatics meeting

26 January 2010

EMERALD will host a thematic workshop at the 6th annual Integrative Bioinformatics (http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010/index.php) which will take place in Cambridge, UK, on March 22nd, 2010.

The focus of the workshop is to discuss and illustrate the importance of microarray data quality and will sum up the work done by the project over a three year period. Presentations will highlight efforts on the implementation of quality metrics and standards to and how experience from this project can be applied to new high throughput array technologies.

Tentative agenda March 22:
10.00 – 10.05  Welcome
Martin Kuiper, NTNU, Norway

10:05 – 10.30  Progress on transformation and normalization ontology
James Malone, EBI, UK

10.30 – 11.00  NIST SRM 2374: A Certified Reference Material Designed to Support Confidence in Gene Expression Measurements
Marc Salit, NIST, US

11.00 – 11.30  Microarray Quality Metrics
Audrey Kauffmann, European Bioinformatics Institute, UK

11.30 – 12.00  What have we learned from the EMERALD project and how can this knowledge be used for “new” high throughput technologies (Minimum Information about a High-throughput Sequencing Experiment – MINSEQE)

Alvis Brazma, European Bioinformatics Institute, UK

 

For registration (the registration for the EMRALD session is free of charge) and the most recent inforamntion about the IB2010 meeting and the EMERALD session can be found at the IB2010 web page: http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib2010/index.php

 

 

Summary of the EMERALD QC web survey

17 August 2009

The goal of this survey was to gain insight into procedures, platforms, and needs of the microarray users community. The focus was both on commercial GeneChip arrays and all sources of cDNA and oligonucleotide microarrays. The survey was geared to gather information anonymously from academic, pharmaceutical, and commercial laboratories, which use microarray technologies routinely.
The main conclusions of the survey were:
In general, microarray users seem to be satisfied with the quality of the data they obtain, either by themselves or though a core facility. Most participants use commercial platforms like Affymetrix, Agilent and Illumina and run about 100 samples a year (this is not much, indicating that many scientists do their analysis by themselves instead of as a service in a core facility). However, still a quite large proportion of the arrays processed are homemade two-color arrays.
Almost all participants comply with MIAME and submit their data to a public repository and most are positive to reporting using a controlled vocabulary instead of free text.
For quality control, most of the participants seem to use regular Bioconductor packages and visual inspections of plots/graphs. But the participants are open to use other software if it is recommended or shown to be better. Some use spike-in RNA as control and many are positive to that, but for some the added price may be prohibitive.
When the quality is not good (which most report having seen occasionally), they try to correct for this or reject the sample. The most important factor giving bad results seems to be RNA quality.
A more extensive summary of the result from the survey can be found here.

 

EMERALD Micoarray Quality Newsletter Nr.3 available

17 August 2009

The third issue of the EMERALD Microarray Quality Newsletter is now available and can be downloaded here.

To subscribe for furure issues, please fill inn the form above at this page.

 

Advances in Microarray Technology, 18-20 May, 2009, Stockholm, Sweden

06 April 2009

EMERALD will organize a symposium in collaboration with the Advances in Microarray Technology conference, to discuss implications for new technology and data quality. Presentations will highlight efforts on the implementation of quality metrics, ontologies and standards to new high throughput array technologies. The symposium will take place together with other pre-conference sessions at Stockholm International Fairs & Congress Centre, at Monday May 18.

More information about the meeting can be found here.

Detailed information and registration to our symposium can be done here.

Confirmed speakers in our session are:

Ulf Landegren, University of Uppsala, Sweden
Audrey Kauffmann, European Bioinformatics Institute, UK
Jochen Schwenk, KTH Royal Institute of Technology, Sweden
Jörg Hoheisel, Deutsches Krebsforschungszentrum, Germany

Marc Salit, NIST, US

Alvis Brazma, European Bioinformatics Institute, UK

 

EMERALD Micoarray Quality Newsletter Nr.2 available

04 January 2009

The second issue of the EMERALD Microarray Quality Newsletter is now available and can be downloaded here.

To subscribe for furure issues, please fill inn the form above at this page.

 

New discussion forum open

10 December 2008

A duscussion forum related to microarray data quality metrics, ontology development and external standards issues are now opened at our web page. See menu at left side of this page or click just click here to enter.

 

EMERALD Micoarray Quality Newsletter Nr.1 available

07 November 2008

The first issue of the EMERALD Microarray Quality Newsletter is now available and can be downloaded here.

To subscribe for furure issues, please fill inn the form above at this page.

 

EMERALD Workshops/Sessions to come in November and December

04 November 2008

1. EMERALD will organize a workshop at the 4th EMBO Conference: From Functional Genomics to Systems Biology, to discuss and illustrate the importance of microarray data quality for systems biology. Presentations will highlight efforts on the implementation of quality metrics, the production of benchmark datasets and the development of checklists to archive experimental metadata to facilitate data analysis and integration.

Workshop topics:

Microarray data quality and quality metrics
Network inference and data quality
External standards / benchmarks for microarray studies
MIBBI: checklists for biological experiments

Key note speaker is John Quackenbush, Dana-Farber, Harvard, US.

The workshop will take place on Tuesday November 18, 13:00-17:00.

The full program can be found here.

 

2. EMERALD will organize a session at CAMDA08. The focus of the workshop is to discuss and illustrate the importance of microarray data quality. Presentations will highlight efforts on the implementation of quality metrics, the production of benchmark datasets and the development of ontologies to facilitate data analysis and integration.
The session will be held December 5th.
Already confirmed keynote speakers for this session are Ernst Wit (University of Groningen, NL) and Walter Liggett (NIST, US).

The full program can be found here.

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Invitation to participate in EMERALD Microarray Survey

23 September 2008

The goal of this survey is to gain insight into procedures, platforms, and needs of the microarray users community. The focus is both on commercial GeneChip arrays and all sources of cDNA and oligonucleotide microarrays. The survey is geared to gather information anonymously from academic, pharmaceutical, and commercial laboratories, which use microarray technologies routinely.

Laboratories and bioinformaticans that use these technologies are invited to participate in this study by filling out a web based survey form. The form can be found directly through this link:

http://kvass.itea.ntnu.no/eval/login.do?externalid=2021-14551abbr

The form is used to collect information such as instrumentation, wet lab protocols, data analysis protocols, quality control protocols and other data analysis issues.

Please note that this is not a sales or marketing survey.

The results of the survey will be made freely available to the microarrays community following analysis of the data, through this web page.

We appreciate your participation in this study.

 

EMERALD Sponsored Data Transformation Ontology Workshop, 2008

22 September 2008

As part of the ongoing effort to create a data transformation ontology, an EMERALD sponsored workshop which will take place at the European Bioinformatics Institute, Cambridge between 3-7th November, 2008. More information, including the current agenda, can be found here.

 

3rd Functional Genomics Conference, Functional Genomics and Desease, Innsbruck, Austria

25 April 2008

EMERALD will host a session at the ESF Functional Genomics Confernce in Innsbruck, Austria - October 1-4 2008. The session wil forcus on microarrays and clinical applications. More information about the meeting and our session can be found here. Deadlines are, 30 May 2008 for abstract submissions and 30 June 2008 for early registration.

 

EMERALD Workshops in 2008

25 January 2008

EMERALD will during 2008 host several workshops in associations with European meetings/conferences. An updated overview can be found here. Further information related to this workshops will occur at this webpage in near future.

 

Data Analysis Workshop

01 October 2007

CAMDA 2007 - EMERALD Data Analysis Workshop Session: Three travel bursaries for PhD students available. EMERALD will sponsor a workshop Session in Valencia, December 13, 2007, hosting by CAMDA 2007, to discuss ways to benchmark preprocessing techniques on public data like from MicroArray Quality Control (MAQC). More information can be found here.

 

EMERALD Sponsored Data Transformation Ontology Workshop, 2007

20 September 2007

Dates have been confirmed for the EMERALD sponsored workshop which will take place at the European Bioinformatics Institute, Cambridge between 5-9th November, 2007. More information, including the current agenda, can be found here.

 

EMERALD-MGED 10: Three funded bursaries for PhD students from the EU member countries

25 April 2007

For the Annual Microarray and Gene Expression Data Society meeting MGED 10 in Brisbane, September 2007, we are happy to announce three bursaries for PhD students from the European Union member countries, funded by EMERALD. More information can be found here.

 

EMERALD-MGED 10 Session Workshop

25 April 2007

EMERALD will co-sponsor a session on microarray quality issues at the Annual Microarray and Gene Expression Data Society meeting MGED 10 in Brisbane, September 2007. Talks will address the development and implementation of Quality Assurance and Quality Control measures in research, service, and diagnostics. It will be discussed how quality metrics can help to improve the selection and development of high quality datasets, and what particular quality criteria such metrics should address. The MGED10 session will be the first of a series of topical workshops that will be organized in the years to come, most of them linked to European meetings related to microarray data or technology.