Process Description

Create a Design File from MiniML

This process imports information stored in the Gene Expression Omnibus (GEO) miniML format and uses this information to generate a valid Experimental Design File (EDF) needed for downstream JMP Genomics processes.

What do I need?

To run the Generate Design File from MiniML process, you must first download and decompress a data set from the GEO website.

Note: The current implementation assumes that the raw data files are stored in external data files. Files in which the data is stored directly in the .xml file (using the Internal-Data tag, for example) are not currently supported.

In the example that follows, the GSE6930_family.xml.tgz compressed data set was downloaded from the GEO FTP server and saved to the GEO directory created within the Sample Data directory that is included with JMP Genomics. The data set was unzipped and all of the files were saved to the GEO directory. Files in this directory are listed below.

Most of the files are .txt files and contain the primary microarray data. The zipped file is still present. Note the presence of the GSE6930_family.xml file. This file contains the information needed to build the EDF.

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 Create a Design File from MiniML output documentation for a detailed description of the output of this process.