Instructions for performing RMA analyses in Expression console

1. The RAW data should come as Affymetrix .CEL files. Save the files and remember their location.

2.Go to If you don’t have an account click “register” and create an account. Otherwise, log in.

3.Use the search tool to look up Affymetrix Expression Console. (The software used to be free and readily downloadable from Affymetrix. It appears you have to inquire about it now.)

4.When you first start the software, you should be asked which folder the program should look for library files in. Specify a folder and make sure you save library files into that folder.

5.When not using the axolotl array, the download library files and download annotation files options under the “File” tab will allow you to readily download files.

6.When using the axolotl array you will need to download the Library files for the corresponding genechip from here. Make sure they are unzipped and saved in the folder that Expression Console searches for library files.

7.Select File->New study

8.A box should appear. In that box, click “Add Intensity Files”

9.Select all the .CEL files that are associated with chips that are part of the study.

10.The file names of those CEL files should be added inside the box.

11.Make sure all the CEL files are checked.

12.Select Analysis->3’ Expression Arrays->RMA

13.After running the analysis, a new list of files should be created, listed in the box, and checked. These are .CHP files and represent the normalized data.

14.Click “Uncheck all” and then click “Check Group” and select “RMA-Group 1”, the .CHP files should all be selected.

15.Select Export->Export Probe Set Results (pivot table)to Txt

16.This will open a save prompt. Save your results as a .txt file.

17.The new .txt file can be opened in Excel. This file is the normalized data and should be ready for analysis.