Process Description

Illumina Expression Input Engine

The Illumina Expression Input Engine imports expression data from a Sample Gene Profile table contained in a text file generated by Illumina®’s BeadStudio Gene Expression module into a SAS data set, and creates a corresponding Experimental Design Data Set (EDDS) and Annotation Data Set. These data sets can subsequently be used as input for the advanced JMP Genomics analytical processes.

What do I need?

The Illumina Expression Input Engine can import data from either:

•

the Exported file produced by the BeadStudio Gene Expression Module, or

•

the Final Report file generated by the BeadStudio Report Wizard.

Two text files are needed to import data from BeadStudio:

•

SampleGeneProfile.txt, which contains the data from an Illumina Sample Gene Profile table and is used in the following example. This file, which is included with BeadStudio as a demo file, is shown below.

•

A file that contains data from an Illumina Samples table. The Samples.txt file used in the following example is shown below.

Both files were downloaded from the Illumina website and saved in a directory, labeled Illumina, that was created in the Sample Data folder included with JMP Genomics.

The following example uses the BeadStudio demo files shown above. The files were downloaded from Illumina and placed in an Illumina folder created in the Sample Data folder. Please contact Illumina for more information about this data set.

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

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the Illumina Expression Input Engine output documentation for detailed descriptions.