Instructions for performing RMA analyses using Partek Genomics Suite

1.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 a folder that Partek can access.

2.Open Partek Genomics suite.

3.Select File->Import->Affymetrix->CEL files

4.Select the .CEL files that correspond with chips in the current study.

5.Select Use RMA

6.Click Import

7.The first time this is done, the program may ask to specify a library folder, select the folder that has the .CDF and .CLF files.

8.The data should open as a spreadsheet in Partek. Partek is capable of further downstream analyses. Each row should be one chip. Many useful tools can be found in the “View” and “Stats” tabs. The Gene Expression Workflow may also be veryWithin the Gene Expression workflow is an “Add Sample Attributes” option which will allow the chips to be sorted into experimental groups for statistical analyses.

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 www.affymetrix.com 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.

Ambystoma Community:

Salamanders in Research
Salamanders have served as model organisms for more than a century. A majority of the earliest embryological and morphological analyses of vertebrate development were conducted using salamander embryos. Today, salamanders continue to be the best animal models for several areas of research and a new generation of researchers are adopting salamanders – and in particular the Mexican axolotl - as their primary animal model. This webpage provides links to projects that are developing resources to enhance the salamander models.

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