Bioinformatics workshops

Microarray Analysis Focusing on Affymetrix Exon arrays

The Bioinformatics Institute at the University of Auckland will hold a small group tutorial on the use and analysis of Affymetrix exon arrays on Thursday 10th Mach at 1pm-3pm. This covered the basics of array analysis and an overview of exon array analysis, included tools that can be used, the types of results to expect, and analysis pitfalls. Material and data form this workshop can be found in the workshop slides and data page of this web site


1st July 2011

Bioinformatics workshop

  • An introduction to basic -omic technologies of arrays and next generation sequencing
  • An introduction to concepts such as multiple testing, family-wise error rate correction –vs- false discovery rate control, why pooling rarely works well for -omics experiments
  • A simple example of a cell culture Affy microarray experiment (describing from lab biology through to QC, normalisation, simple LIMMA, then pathways analysis based on a gene list)
  • A basic RNA seq analysis
  • A discussion of other types of –omics and bioinformatics such as meta-genomics, re-sequencing, proteomics, metabolomics, imageomics


Bioinformatics for non-specialist bioinformaticians

The Bioinformatics Institute is holding a number of short courses in October 2010 that are intended for REAL beginners in the world of genomics and bioinformatics.

Maurice Wilkins Centre Bioinformatics Workshop


This interactive workshop provides an introduction to bioinformatics, microarrays and next generation sequencing . It will be held on Wednesday 20th October 1-3pm, in the 5th floor seminar (room 501-505), Grafton Campus, University of Auckland, run by Cris Print, Peter Tsai, and Liam Williams. It will be followed by nibbles and tea/coffee.

This workshop is aimed at REAL beginners in the world of genomics and bioinformatics. Topics include:

  • Basic description of the changing microarray and sequencing technologies
  • How this type of work can be done in Auckland
  • Experimental design
  • Basic data analysis concepts
  • Pathway analysis
  • Ideas for discussion about writing successful grant applications and papers in this field

The NZ eResearch Conference will contain two hands-on data analysis workshops for beginners: (i) gene expression data, (ii) next generation sequencing data

To attend this conference, including these workshops and the conference dinner, please register at Registration fee for conference and workshops is $170 (students) and $295 (non-students). This fee will include up to 4 hours assistance from a skilled bioinformatician as you analyse your own data after you have completed the workshops.


Workshop 1:Introduction to the analysis and exploration of gene expression data (1pm - 4pm, Tuesday 26th October, co-ordinated by Cris Print and Mik Black):

- Designed for researchers who have an aptitude for data analysis but who have no formal training in bioinformatics or statistics.

- Focus on Affymetrix data but will also be relevant to other data types.

- Introduction to a simple one-button quality control and analyses application.

- The user-friendly GenePattern platform.

- Basics of more complex data exploration methods using.



Workshop 2:Introduction to the analysis of next generation sequencing data (1pm – 4pm, Wednesday 27th October, co-ordinated by Mik Black and Cris Print)

- Designed for researchers who have no formal training in bioinformatics.

- Focus on Roche 454 next generation sequence data but also relevant to other next generation sequence data types.

- Quality control and format conversion.

- Basic assembly and visualisation.


Workshop for beginners wishing to learn the basics of "R"

This workshop will be held on Thursday 28th October 9:00am - noon, Room 303-B75, City Campus, run by Thomas Lumley and James Curran. This workshop has no charge, however please RSVP since spaces are limited.


The statistical and bioinformatics environment named “R” is at the core of most analyses of gene expression data and next generation sequencing data. It is an incredibly powerful open source platform. Some people suggest that any group working on high content data should have at least one team member who can use “R”. However, “R” can seem intimidating at first and does take a few hours to learn. This workshop will be useful for researchers with no prior experience who want to get to grips with "R".

The Bioinformatics Institute Maurice Wilkins Center Faculty of Medical and Health Sciences Department of Statistics