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MaPhySto
Centre for Mathematical Physics and Stochastics
Department of Mathematical Sciences, University of Aarhus

Funded by The Danish National Research Foundation



Workshop on

Statistical Aspects of Microarray Data

Thursday 20 - Saturday 22 February, 2003
Department of Mathematical Sciences, University of Aarhus

Auditorium F, Building 534

Summary

Microarrays can provide a broad picture of the state of a cell by monitoring the expression level of thousands of genes at the same time. As such the technique can give valueable information on many biological processes. In particular in relation to tumors a precise classification is of importance for finding the optimal treatment.

Microarray data poses many interesting statistical problems. The raw data consists of an image of scanned pixel values and the location of a particular gene must be identified. Often there will be outliers in the data that need to be detected. A fundamental but very difficult question is the precise translation of a pixel value to the number of molecules present. Due to the variation in the production of the chips and the variation in the preparation of the samples the data from two arrays cannot be compared before a normalization has been made. This seems to be a non-trivial task and unless done very carefully one may introduce systematic errors. There seems to be a need of establishing an accepted standard for the normalization process. Coming to the estimation of the actual expression level of a gene one is still lacking a systematic study delineating the part of the variance due to the measurement technique and the part due to biological variation. Also for the Affymetrix system it is a very interesting question how to use best the information in the mismatch probes. When comparing two groups and searching for genes that are differentially expressed in the two groups one faces the problem of multiple comparisons. Obviously, if only a small number of genes participate in the difference between the two groups and we have no prior information as to what group of genes the differentially expressed genes belong to we are facing a problem when the chip contains a huge number of genes. Many microarray studies are used for classification and clustering. The maximum likelihood classifier based on independent normally distributed values seems to be one of the better choices. The assumptions for using this classifier needs to be checked and perhaps the modelling of the distributions can be improved. Underlying the above points are also the problem of designing the experiments so as best to extract the information.

It is the intention of the workshop to cover most of the aspects mentioned above.

Organizing Committee:

Jens Ledet Jensen (University of Aarhus), Chairman
Mathisca de Gunst (EURANDOM, Eindhoven/Free University of Amsterdam)
Mats Rudemo (Stochastic Centre, Gothenburg)
Michael Sørensen (University of Copenhagen)

The workshop is co-funded by a grant from the Danish National Science Foundation.

Programme:

Wednesday February 19
19:00-21:00: Registration and get-together
Thursday, February 20
08:30-09:30: Registration
09:30-09:40: Welcome
09:40-10:25: Claus Mayer (Rowett Research Institute, Aberdeen, Scotland): Least trimmed squares methods for microarray normalization
10:40-11:10: Coffee/tea
11:10-11:55: David Edwards (NOVO Nordisk, Denmark): On the pre-analysis of one-channel cDNA microarray data
12:10-13.30: Lunch
13:30-14:15: Torben F. Ĝrntoft (Molecular Diagnostic Laboratory, Aarhus, Denmark): Microarrays, basic principle and use in medical research
14:30-15:15: Yudi Pawitan (Department of Medical Epidemiology, Karolinska Institute, Stockholm): Survival analysis using gene expression data
15:30-16:00: Coffee/tea
16:00-16:45: Mark van der Laan (University of California, Berkeley): Statistical inference with gene expression data
Friday, February 21
09:10-09:40: Mette Langaas (Department of Mathematical Sciences, Norwegian University of Science and Technology, Trondheim, Norway): Estimating the number of genes truly differentially expressed
09:50-10:20: Jörg Assmus (Department of Mathematics, University of Bergen, Norway): On the problem of significant p-values for gene expressions
10:30-11:00: Coffee/tea
11:00-11:45: Jelle Goeman (Leiden University Medical Center, The Netherlands): A global score test for differential expression of groups of genes in high-dimensional microarray data
12:00-14.00: Lunch
14:10-14:55: Mats Rudemo (Mathematical Statistics, Chalmers University of Technology, Göteborg, Sweden): Empirical Bayes analysis of variance models for microarray data
15:10-15:40: Coffee/tea
15:40-16:25: Ernst Wit (Department of Statistics, University of Glasgow, U.K.): Hidden Markov modelling of genomic expression interactions
16:40-17:25: Arnoldo Frigessi (Norwegian Computing Center, Oslo, Norway): Towards a comprehensive statistical model of cDNA microarrays
18:30: Workshop dinner
Saturday, February 22
09:00-09:45: Rafael Irizarry (Department of Biostatistics, Baltimore, USA): Getting usable data from microarrays: The role of statisticians
10:00-10:30: Coffee/tea
10:30-11:15: Steen Knudsen (Technical University of Denmark): A new non-linear normalization method for reducing variablility in DNA microarray experiments
11:30-12:15: Volkmar Liebscher (Institute of Biomathematics and Biometry, München, Germany): Stochasting modelling and quality control for gene expression data
12:30-13.15: Lunch
13:15-14.00: Anja von Heydebreck (Max-Planck-Institute for Molecular Genetics, Division of Computational Molecular Biology, Berlin, Germany): Error modelling, data transformation and robust calibration for microarray data
14:15-14:45: Coffee/tea

Registration Fee

The registration fee, covering lunches, is DKK 400, payable in cash in Danish currency upon arrival at the workshop.

List of Participants

Abstracts



More Information

Do not hesitate to contact the MaPhySto secretariat (at maphysto@maphysto.dk) for more information.

(This announcement in [ postscript-format | pdf-format ])


This document, http://www.maphysto.dk/oldpages/events/MicroArr03/index.html, was last modified January 19, 2004. Questions or comments to the contents of this document should be directed to maphysto@maphysto.dk.