Instructions for performing RMA analyses using Partek

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.