S3RI Seminar - BASiCS: dealing with technical and biological noise in single-cell expression data, Catalina Vallejos (Alan Turing Institute & UCL) Seminar
- Time:
- 14:00 - 15:00
- Date:
- 16 November 2017
- Venue:
- Room 8033, Lecture Theatre 8B, Building 54, Mathematical Sciences, University of Southampton, Highfield Campus, SO17 1BJ
For more information regarding this seminar, please email Professor Dankmar Bohning at D.A.Bohning@soton.ac.uk .
Event details
Single-cell RNA-sequencing (scRNA-seq) has transformed the field of transcriptomics, providing novel insights that were not accessible to bulk-level experiments. However, the promise of scRNA-seq comes at the cost of higher data complexity. In particular, a prominent feature of scRNA-seq experiments is strong measurement error, reflected by technical dropouts and poor correlations between technical replicatres. These effects must be taken into account to reveal biological findings that are not confounded by technical variation.
In this talk, I will describe some statistical challenges that arise when analyzing scRNA-seq datasets. I will also introduce BASiCS (Bayesian Analysis of Single Cell Sequencing data), a Bayesian hierarchical model in which data normalization, noise quantification and downstream analyses are simultaneously performed. BASiCS exploits experimental design to disentangle biological signal from technical artifacts. This includes: (i) a vertical integration approach, where a set of technical spike-in genes is used as a gold-standard and (ii) a horizontal integration framework, where technical variation is quantified by borrowing information from multiple groups of samples. Using control experiments and case studies, I will illustrate how BASiCS goes beyond traditional differential expression analyses, identifying changes in cell-to-cell gene expression variability between groups of cells (such as experimental conditions or cell types). Finally, I will describe ongoing extensions to account for the confounding between mean and variability that is often observed in scRNA-seq datasets.
The seminar will also be available via a live web-cast at
https://coursecast.soton.ac.uk/Panopto/Pages/Viewer.aspx?id=c43f33bd-b7b5-46f9-ad6a-bf16a3a35aea
Speaker information
Dr Catalina Vallejos , The Alan Turing Institute & UCL. Research Fellow Department of Statistical Science