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Introduction
One of the most basic functions in
AltAnalyze is to summarize data from a typical
gene expression microarray experiment. Unlike
more advanced features (e.g., analysis of splicing
with exon or exon-junction data), this option
allows you to easily get statistics and annotations
for your dataset without having had to had prior
experience with analyzing microarray data. The
below steps will walk you through performing a
basic gene expression analysis with AltAnalyze
using sample data.
Downloading
AltAnalyze
AltAnalyze
can be downloaded for multiple operating systems
from http://www.AltAnalyze.org.
Once you have downloaded the compressed archives
to your computer, extract these to an accessible
folder on hard-drive (e.g., your user account).
Downloading
Sample Data
Affymetrix
CEL files
AltAnalyze can directly process Affymetrix CEL
files. Click here
to download sample data and obtain expression
values.
Running
AltAnalyze
Now you are ready to process
your raw input files and obtain alternative probe
sets with splicing and functional annotations.
To proceed:
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1)
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Open
the AltAnalyze_v1beta folder and select the
executable file "AltAnalyze". In Windows,
this file has the extension ".exe". If you
are working on a Linux machine or are having
problems starting AltAnalyze, you can also
start the program directly from the source
code. |
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2) |
(AltAnalyze:
Introduction) In the resulting introduction
window, select "Begin Analysis". |
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3) |
(AltAnalyze:
Main Dataset Parameters) Select the species
type "Mus musculus" and "Continue". |
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4) |
(AltAnalyze:
Main Dataset Parameters) Select the "CEL files"
button and the array type "Affymetrix 3’ Array". |
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5) |
(AltAnalyze:
Select CEL files for APT) For dataset name,
type in "mESC_differentiation", select
the directory containing your CEL files and
select a folder where you want to save the
result folders and select "Continue". |
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6) |
(AltAnalyze:
Expression Analysis Parameters) In addition
to accepting the default parameters, select
"run immediately" under the option
"Perform GO-Elite GO/pathway analysis"
and select "Continue". |
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7) |
(AltAnalyze:
Pathway Analysis Parameters) Accept all of
the default parameters by clicking "Continue".
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8) |
(AltAnalyze:
Assign CEL files to a Group) Type in the group
name for each sample. |
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9) |
(AltAnalyze:
Establish All Pairwise Comparisons) Selects
the groups to compare. |
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10) |
A
new window will appear that displays the progress
of the analysis. Analysis of the sample dataset
should take approximately 20 minutes, but
can take longer depending upon the machine
and operating system. When finished, AltAnalyze
will display a new pop-up window, informing
the user that the analysis is complete. If
analyzing multiple experimental groups, these
will be run in succession. A new results window
will appear that contains links to online
help and other resources. |
Interpreting
the Results
Proceed
here.
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