Process Description

Export to GSEA Format

The Export to GSEA Format process exports an input data set and an experimental design data set (EDDS) to files to be used by GSEA (Subramanian, Tamayo, et al. 2005; Mootha, Lindgren, et al. 2003). Output files include a .txt file containing expression measurements and one or more .cls files for phenotypes.

Please refer to http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats for more information about these file formats.

Note: This process is considered experimental.

What do I need?

Two data sets are required to run the Export to GSEA Format process:

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An Input Data Set that contains all of the numeric data to be analyzed. The drosophilaaging.sas7bdat data set from the Drosophila aging experiment of Jin, et al. (2001), described in Drosophila Aging Experimental Data, serves as an example, and is shown below. It has 48 data columns and 100 rows. Note that this is a tall data set; each probe corresponds to one row whereas each column corresponds to a separate experimental condition.

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An Experimental Design Data Set (EDDS). This data set tells how the experiment was performed, providing information about the columns in the input data set. The drosophilaaging_exp.sas7bdat EDDS is shown below. The data set contains 8 columns and 48 rows. Experimental variables include age, line, and sex of the flies. Note that one column in the EDDS must be named ColumnName and the values contained in this column must exactly match the column names in the input data set.

The drosophilaaging.sas7bdat and drosophilaaging_exp.sas7bdat data sets are located in the Sample Data\Microarray\Scanalyze Drosophila directory included with JMP Genomics.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

Refer to the Export to GSEA Format output documentation for detailed descriptions of the output of this process.