DomainGraph Documentation
Contents
How to obtain the appropriate file for Differential Expression Analysis...
... using AltAnalyze
AltAnalyze generates a file named *-DomainGraph.txt, which is specifically designed for further analysis using DomainGraph. This file can be used to analyze a particular network of interest. It can also be used for the general analysis of differential expression within the data.
- Download AltAnalyze here.
- Unpack and start the program.
- Follow the steps for Exon Expression Analysis.
- You will receive a *-DomainGraph.txt file, which is stored in the AltAnalyze output folder (under the AltAnalyze program folder).
How to obtain the appropriate files for Single Experiments...
... using the Affymetrix Power Tools (APT)
- Download APT and the library files from Affymetrix.
- Install APT and start the APT Command Prompt.
- Type the following command (using correct pathnames) in the apt console (this example uses RMA for normalization):
apt-probeset-summarize -a rma-sketch -a dabg -p HuEx-1_0-st-v2.r2.pgf -c HuEx-1_0-st-v2.r2.clf -b HuEx-1_0-st-v2.r2.antigenomic.bgp --qc-probesets HuEx-1_0-st-v2.r2.qcc -o OutputDirectory --cel-files YourCelfiles.txt
- You will receive a DABG file (containing the probeset ids and corresponding p-values) and an expression file (containing probeset ids and corresponding expression values), which you can import into DomainGraph.
... using Affymetrix' Expression Console
- Download the Expression Console from Affymetrix.
- Install Expression Console and start the program.
- Set up a new study
- Press the 'Add Intensity Files' button to select the CEL files you want.
- Go to the Menu, select 'Analysis -> Exon Level -> Core RMA'.
- You will receive a DABG file (containing the probeset ids and corresponding p-values) and an expression file (containing probeset ids and corresponding expression values) in the folder where your CEL files are stored.
