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EVENT: Normalisation of RNA-Seq Data: Are the ERCC Spike-In Controls Reliable?

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Today's date is Tuesday, March 02, 2021
Normalisation of RNA-Seq Data: Are the ERCC Spike-In Controls Reliable? Other events...
Professor Terry Speed is a Senior Principal Research Scientist and lab head in the Bioinformatics Division of the Walter and Eliza Hall Institute of Medical Research. He is recognised as one of the world's leaders in the relatively new field of bioinformatics. He has more than 40 years of experience in statistics, specialising in the design and analysis of studies in genetics and genomics. A fellow of the Australian Academy of Sciences, Professor Speed was recently elected as a fellow of the Royal Society of London, and in 2013 he was awarded the Australian Prime Minister's Prize for Science.

The External RNA Control Consortium (ERCC) developed a set of 92 synthetic polyadenylated RNA standards that mimic natural eukaryotic mRNA. The standards are designed to have a wide range of lengths (250-2,000 nucleotides) and GC-contents (5-51%). The ERCC standards can be spiked into RNA at various concentrations prior to the library preparation step and serve as negative and positive controls in RNA-Seq. Ambion commercialises spike-in control mixes, ERCC ExFold RNA Spike-in Control Mix 1 and 2, each containing the same set of 92 standards, but at different concentrations. We investigate the use of the ERCC spike-in controls for two main purposes: (a) Quality assessment/quality control (QA/QC) of RNA-Seq data and benchmarking of normalisation and differential expression (DE) methods, and (b) Direct inclusion in between-sample normalisation procedures. We have two RNA-seq data sets which make use of the ERCC controls: a local one concerning treated and untreated zebrafish tissue, and some of the SEQC samples. A variety of normalisation methods will be compared, both using and not using the ERCC controls. One of the methods we discuss is a variant on our recently published RUV-2 method, which uses SVD on negative controls.

This event is free and no RSVP required.
Speaker(s) Professor Terry Speed (joint with Sandrine Dudoit, Davide Risso and John Ngai)
Location Science Library Access Grid Room, UWA
Contact Selynn Chan <[email protected]>
URL https://www.amsi.org.au/speed
Start Wed, 08 Oct 2014 13:00
End Wed, 08 Oct 2014 14:30
Submitted by Selynn Chan <[email protected]>
Last Updated Mon, 25 Aug 2014 11:52
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