Agilent GeneSpringGX 9.0 User Guide
GeneSpring GX 9
Quick Start Guide
The information in this guide is for use with GeneSpring GX 9
...............................................................................................What is GeneSpring GX 9? 1
....................................................................................Where do I get GeneSpring GX 9? 1
.............................................................................Is there a demo experiment I can run? 1
........................................................................................How can I get more Pathways? 9
What is GeneSpring GX 9?
GeneSpring GX is a powerful visualization and analysis solution
designed for use with genomic expression data. It allows you to
display and analyze large data sets on your personal computer.
GeneSpring GX can analyze data from many sources, including
academic, biotechnology, and pharmaceutical organizations.
Where do I get GeneSpring GX 9?
You can download a free evaluation copy of GeneSpring GX that will
be fully active for 15 days. Go to http://genespring.com and follow
the link for “Download FREE Trial”.
If you would like to buy a copy of GeneSpring GX, request a quote
from the website, call +1-800-227-9770 (Option 6) or contact your
Agilent sales representative or distributor.
....................................................................How do I get started with GeneSpring GX 9? 1
..................................................................Where do I get GSEA compatible Gene Sets? 10
.......................................................................Where is my data from GeneSpring GX 7? 10
How do I get started with GeneSpring GX 9?
After installation of GeneSpring GX, you can get started immediately
since it comes pre-loaded with a demonstration experiment to show
you the functionality of GeneSpring GX. There is a project called
“Demo Project” and contains an experiment and results from a study
of HeLa cells that were treated with an unknown compound in a
cancer treatment pilot study. We encourage you to explore this
demonstration project to get to know GeneSpring GX.
Is there a demo experiment I can run?
You can re-create the experiment from the demonstration project,
since the original data you need is provided with the installation. The
data files you need are located in the samples directory of the main
installation folder, usually found in
C:\Program Files\Agilent\GeneSpringGX
Follow the steps below to create a new experiment with the provided
data:
1) Start GeneSpring GX
2) Select the “Demo Project” from the Startup dialog box (or create
a new project)
GeneSpring GX 9 Quick Start Guide 1
3) This will open the project open the experiment that was stored in
this project
4) To create a new project, press the New Experiment icon on the
Toolbar ( ) or select “Project -> New Experiment” from the
menu bar.
5) This will start the new Experiment wizard that will guide you
through the creation of the experiment
6) For the name, use something such as “HeLa cells treatment” to
give it a sensible name
7) Since the data we provided is a Agilent Single Color experiment,
choose “Agilent Single Color” as the Experiment Type.
8) There are two modes of GeneSpring GX, “Guided Workflow” or
“Advanced Analysis”. The Guided Workflow option will provide a
you with full guidance and is a good starting point. Select
“Guided Workflow” for the Workflow Type and press OK.
9) The next window will allow you to import new data files into the
system or use data that had been previously loaded (samples).
For this demonstration experiment we will use new data files.
GeneSpring GX 9 Quick Start Guide 2
10) Select Choose Files to bring up the Choose file dialog. The choose
file dialog will most likely already point to the samples directory in
the main GeneSpring GX installation directory, but if not, point it
to the directory called “Agilent One-color Demo”, which is in
C:\Program Files\Agilent\GeneSpringGX\samples\Agilent Onecolor Demo
By default.
11) Select all .txt files to be loaded and press OK:
•
"US22502705_251209747382_Untreated.txt"
•
"US22502705_251209747387_Untreated.txt"
•
"US22502705_251209747392_Treated.txt"
•
"US22502705_251209747393_Treated.txt"
•
"US22502705_251209747394_Untreated.txt"
•
"US22502705_251209747404_Treated.txt"
12) The application will load the files, extract the expression data and
perform some standard normalizations and transformations. For
the Guided Workflow: Find Significant Differentially Expressed
Genes” the defaults are set as follows:
•
Threshold all values to 5
•
Perform a Median Shift normalization to the 75 percentile
•
Perform a Baseline transformation using the median of all
samples
13) These are sensible normalization for many experiments and will
provide a good starting point. In the advanced analysis workflows
you can change these normalization and transformation settings
to more appropriate settings for your experiment.
14) After the samples have been loaded and processed, the Guided
Workflow wizard will appear and show a summary of the data
with a box plot of the data distribution of the 6 samples and an
outline of the steps that will be performed on the left side.
GeneSpring GX 9 Quick Start Guide 3
15) The guided workflows are controlled by pressing the <Next>
button to go to the next step. By pressing the <Back> button you
can go back and make some modifications. Press the <Next>
button to continue
16) The next window is where we let the program know which
samples are the treated samples and which as the untreated
samples. This is done by adding an “Experimental Parameter” and
pressing the <Add Parameter> button.
17) The filenames are pretty descriptive so it is easy to figure out
which samples are treated and which are untreated. In the Add
Parameter window, make “Treatment” the parameter name and
type the values “Untreated” and “Treated” in the Parameter
Values columns. (Hint: Select the three samples that need the
GeneSpring GX 9 Quick Start Guide 4
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