Workshops

The Bio2 facility offers Biostatistics and Bioinformatics training and advice.
Workshops and consultations are free with facility membership.
Non-members can also register for individual workshops.

March and April Workshops

Please register for the workshops by filling in the workshop registration form and sending it to the Bio2 Facility Officer. Workshops are free with Bio2 facility membership , however, members should still register for the workshops.

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Statistical Analysis with GraphPad Prism

This series of four workshops provides research students with a theoretical and practical introduction to statistical analysis. No previous experience with the software is assumed. Attendees may bring their own laptops (with GraphPad Prism installed) or use the computers in the lab.



Workshop 1: Types of Variables and Distributions

Understanding the type of variable and its distribution is fundamental in choosing the correct statistical test. In this workshop, we will examine the different types of variables contained in an experimental data set. We will look at plotting/determining the distribution of continuous variables (normal, lognormal and skewed), outlier analysis and paired data. Other common distributions, binomial and Poisson, will be discussed as well as the application of the central limit theorem. The appropriate descriptive statistics for particular types of variable/distributions will be outlined. The aim of the workshop is also for the attendee to become proficient at formatting data tables of different types, performing analyses and creating graphs and layouts.

Date: Thursday, 16th March and Friday, 17th March, 2017
Time: 9.30am-12pm
Venue: Leeuwenhoek lab, W102, Anderson Stuart Building, F13

Workshop 2: Choosing a Statistical Test

This workshop covers the underlying concepts involved in the application of statistical tests including hypotheses, significance, Type I/II errors and P-values. It will focus on experimental designs involving a categorical variable with two groups where the outcome is either numeric or categorical. The aim is to understand the steps in deciding upon an appropriate statistical test and develop strategies for when the choice isn’t clear (e.g. unable to test assumptions because of small sample size). Topics covered include: t test, Mann-Whitney test, parametric vs non-parametric, paired data, Fisher’s exact test/ chi-square test / chi-square test for trend, applying the central limit theorem when choosing a statistical test. We will also look at analyses involving two numeric variables – regression and correlation.

Date: Thursday, 23rd March and Friday, 24th March, 2017
Time: 9.30am-12pm
Venue: Leeuwenhoek lab, W102, Anderson Stuart Building, F13

Workshop 3: Sources of Variation


We will look at the sources of variation in laboratory and clinical research. Many studies are designed to examine the variation in response to an intervention or treatment, however, variation from other sources can obscure the effect or produce a misleading result. Experimental designs and considerations used to improve the power and validity of a study will be discussed. Comparing the variation within groups to the variation between groups is the basis of ANOVA, a commonly-used statistical test for identifying differences more than 2 groups. This workshop also looks at the different approaches for identifying differences between more than 2 groups and the challenges of multiple comparisons. We will explore more complex types of analyses, i.e. multivariate analysis, and the software needed to perform them.

Date: Monday, 27th March and Thursday, 30th March, 2017
Time: 9.30am-12pm
Venue: Leeuwenhoek lab, W102, Anderson Stuart Building, F13


Workshop 4: Significance vs Importance

Hypothesis –testing is an important part of statistical analysis, however, estimation can provide valuable information about the size of an effect. This workshop will focus on the estimation of population parameters from a sample and the calculation and interpretation of confidence intervals. Understanding effects sizes is also useful for determining sample sizes and we will look at the theory and practice of calculating the power of a study. Presentation of quantitative data and statistical analysis in a thesis or paper will also be discussed.

Date: Thursday, 6th April and Friday, 7th April, 2017
Time: 9.30am-12pm
Venue: Leeuwenhoek lab, W102, Anderson Stuart Building, F13



Multivariate Analysis


Multivariate analysis allows us to make sense of complex systems. An array of methods have been developed to simultaneously model multiple variables. This workshop focuses on two approaches - multiple regression models and Factor (and Principal Components) analysis. The workshop will cover the theory, aims, assumptions and interpretations of these analyses. We will also perform two analyses using these methods. The workshop assumes a basic understanding of statistics and the SPSS program.

Date: Monday 3rd April, 2017
Time: 9.30am-12pm
Venue: Leeuwenhoek lab, W102, Anderson Stuart Building, F13

Previous Workshops

Bioinformatics week

The programming language R is a powerful and open-source tool for Bioinformatics analysis. This series of workshops provides an introduction to R and its use in analysis of gene expression in Bioconductor packages such as limma and DESeq2. Register for individual workshops or the entire series.

Introduction to R

The statistical and graphical programming language, R, is widely used because of its power, versatility and free access. This workshop provides a practical introduction to using R/Rstudio. Using the base packages, we will import data sets, perform statistical analyses and write functions. Another aim is to understand the basic data structures in R and how they relate to some of the more specialized data structures in genomics analysis. One of the advantages of R is that it is easily extensible through the installation of additional packages, providing a huge range of statistics and bioinformatics analysis and graphing options. We will use one of the most popular packages, markdown, to document your analysis.

Date: Monday, 21st November, 2016
Time: 9.30am-12pm
Venue: Brennan MacCallum Learning Studio 108, Brennan MacCallum Bldg, A18

Microarray Analysis with Open Source Tools

This workshop focuses on the analysis of oligonucleotide array data, from quality-control metrics to identifying differentially-expressed genes.
We will be using some tools from Bioconductor and some previous experience with R is assumed. The workshop will cover:
Generation and interpretation of QC metrics.
Normalisation and summarisation of expression data.
Methods and statistical challenges for identifying differentially-expressed genes.
Design of Microarray experiments.

Date: Tuesday 22nd November, 2016
Time: 9.30am-12pm
Venue: Brennan MacCallum Learning Studio 108, Brennan MacCallum Bldg, A18

Gene Profiling and Discovery with RNAseq

Gene expression analysis with RNA-seq is sensitive, accurate and versatile, but it can also seem daunting to those accustomed to working with RTqPCR or oligonucleotide arrays. This workshop provides an overview of the technology and the considerations in designing a study, with a particular focus on using RNA-seq to study differential gene expression. The steps in the data analysis and how to perform them with open source tools will be covered. Some statistical approaches for identifying the differentially-expressed genes will be outlined. The workshop includes some data analysis using the DEseq2, edgeR and limma packages in Bioconductor/R. The aim is that participants will obtain an overview in performing a RNA-seq analysis, from selecting an appropriate sample preparation method and sequencing protocol, to understanding the statistical approaches for identifying differentially-expressed genes.

Date: Thursday 24th November, 2016
Time: 9.30am-12pm
Venue: Brennan MacCallum Learning Studio 108, Brennan MacCallum Bldg, A18

From Gene Lists to Pathways

A guide to understanding the biological context of differentially-expressed genes or proteins, with the use of open source tools and Ingenuity Pathways Analysis.

This workshop covers annotation of gene lists with up-to-date functional information. The statistical approaches used to understand whether Gene Ontology (GO) terms or metabolic pathways are overrepresented in data sets will be discussed. We will use open source tools to annotate genes and investigate the involvement of GO terms and pathways. The features of a commercially-available program available to Sydney University researchers, Ingenuity Pathways Analysis, will also be outlined and compared to the open source tools. Gene Set Enrichment Analysis, as an alternative to working with lists of genes obtained with an arbitrary threshold, will also be discussed.

Date: Friday 25th November, 2016
Time: 9.30am-12.30pm
Venue: Brennan MacCallum Learning Studio 108, Brennan MacCallum Bldg, A18

Introduction to Meta-analysis

A meta-analysis harnesses the statistical power of multiple studies to develop a conclusion and assists in understanding the variation in effect sizes. This workshop will give an overview of theoretical and practical considerations in undertaking a meta-analysis. We will use open-source tools to perform a simple meta-analysis.

Date: Wednesday 30th November, 2016
Time: 9.30am-12.30pm
Venue: Brennan MacCallum Learning Studio 108, Brennan MacCallum Bldg, A18