Download Tutorial Analyzing Affymetrix® Gene Expression data in GeneSpring

Introduction to Tutorial:
This tutorial provides a hands-on exploration of the variety of GeneSpring GX functionalities
by guiding you through the analysis of an Affymetrix® gene expression microarray dataset.
In doing so, this tutorial aims to demonstrate how to use the tools available in GeneSpring
GX to answer biological questions relevant to the experimental design.
Understanding GeneSpring GX Terminology
Some terms used in the general biological research community have a more
specialized use in GeneSpring GX. A brief definition of each is provided below
to clarify the tutorial instructions. More terminology can be found in the
GeneSpring GX User Manual.
A project is the primary workspace which contains a collection of experiments. The ability
to combine experiments into a project in Genespring GX allows for easy interrogation of
cross-experimental results. For example, you may want to visualize how genes that were
found to be differentially expressed in one experiment are behaving in another experiment
within the project. A project could have multiple experiments that are run on different
technologies and possibly different organisms as well.
A technology in GeneSpring GX contains information on the array design as well as
biological information about all the entities on a specific array type. Technology refers to
this package of information available for each array type, for e.g., Affymetrix HG-U133 plus 2
is one technology, Agilent 12097 (Human 1A) is another and so on. An experiment
comprises samples which all belong to the same technology. A technology initially must be
installed for each new array type to be analyzed.
An entity is a discrete feature measured by microarray analysis such as a probe or probe
set.
A sample contains data from a microarray run for a single biological source.
An experiment is a collection of samples used for a particular research study that are to be
analyzed as a set. In GeneSpring GX, an experiment consists of multiple interpretations
which group these samples by user-defined parameters.
A parameter is a variable in experiments such as treatment type, tissue type, time, or dose.
Parameter values are values assigned to experiment parameters. For example, “Day 14”
could represent a parameter value of the experiment parameter “Time”.
GeneSpring GX 9 Data Analysis Tutorial for Affymetrix data
2