RSS Merseyside Local Group Meeting - High-throughput Gene Expression Data
27th March 2014, 15.00 Room 406, Brodie Tower, University of Liverpool (Building Reference 233, C8)
15:00-16:00 Julia Brettschneider (Associate Professor, Department of Statistics, University of Warwick)
Subset based assessment of high-throughput gene expression data quality
High throughput gene expression measurement is the basis for quantitative research in functional genomics. Microarrays have become standard laboratory equipment for conducting such assays in a genome-wide scale. For experiments that monitor a biological process over the course of time they are a cost efficient alternative to high-throughput sequencing. Such experiments are commonly used to understand the genetic basis of developmental (e.g. embryo growth) and cyclic (e.g. circadian rhythms) processes. The key to reproducible findings are accurate and precise measurements.
We aim to shed more light onto the appropriate use and the interpretation of quality measures for such high-throughput genomic data (e.g. [1], [2]) with special attention to time course experiments. We have developed design-specific methods that allow us to tailor high throughput quality assessment methods to such situations by restricting the quality assessment to appropriate subsets of genes. This method captures relevant quality patterns without being misguided by biological variation. The method can be applied to a range of platforms.
[1] J. Brettschneider et al, Quality assessment for short oligonucleotide arrays (with commentaries and rejoinder), Technometrics 50(3), 2008.
[2] G. Cohen Freue et al, MDQC: a new quality assessment methods for microarrays based on quality control reports, Bioinformatics 23 (23), 2007.
16:00-16:30 Coffee
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