Authors: Penny Nymark (Misvik Biology), Friederike Ehrhart and Egon Willighagen (Maastricht University), Eija Korpelainen (CSC - IT Center for Science, Finland), Pekka Kohonen and Roland Grafström (Misvik Biology)
Introduction
This tutorial will get you started on the basic use of the bioinformatics tool Chipster, an alternative to ArrayAnalysis.org described in other eNM tutorials. It will guide you through the import of microarray data (Affymetrix .CEL files), quality checks, normalization, pre-processing, basic statistical analyses methods and visualization of your data. Chipster is not specific to the nanosafety field, but this tutorial will be focused on the specific needs of nanotoxicological research.
Chipster is an open source user-friendly analysis software for high-throughput data analysis. It offers over 350 bioinformatics tools and it is constantly updated according to the latest state-of-the-art tools and scripts. Users can analyse and visualize data interactively, and share complete analysis sessions and automatic workflows with colleagues. Chipster supports the analysis of over 120 different microarray platforms, including the most common types by Affymetrix, Agilent and Illumina. In addition, Chipster has extensive functions and tools for the analysis of NGS data.
For additional and deeper guidance on how to use Chipster, beyond this tutorial, see the website with manuals and tutorials or contact the Chipster team. The website also includes guidance on how to analyze next-generation sequencing (NGS) data in Chipster.
You can download the tutorial >> here << or see it in the preview window below.