Quick Start Guide
Expression Console™ miRNA Quick Start Guide
The purpose of the Expression Console™ software application is to enable probe set summarization and initial data quality
examination for miRNA 2.0 and future releases expression arrays. Expression Console software takes probe cell intensity files (*.CEL)
and creates probe level summarization files (*.CHP) using the selected algorithm workflow. Probe level summarization files can then
be further analyzed using software applications from GeneChip-compatible™ partners like PartekTM Genomics Suite™ and SpotfireTM.
1.
Download the necessary library files for analyzing your array type if they are not already in the library file directory.
a. Go to the File menu and select Download Library Files.
b. Enter your NetAffxTM email address and password. If you do not have one you will first need to register at our web site.
c. In the NetAffx Library File window check all probe array types that you will be analyzing now or in the future and click the
Download button (e.g., miRNA 2-0 library files). You can always come back and add more library files at a later date.
2.
Create a New Study by selecting File > New Study or by going to the Study tab of the workflow toolbox and selecting Create New
Study. A Study consists of a collection of probe cell intensity files (CEL) and probe level summarization files (CHP) of the same
array type.
A blank Study window is created.
3.
Use the Add Intensity Files button at the bottom of the Study window or click Add Intensity Files in the toolbox to add your
collection of CEL files to the Study.
For Research Use Only. Not for use in diagnostic procedures.
4.
Once the appropriate CEL files have been added, use the check boxes to select the CEL files to be summarized.
5.
Click Run Analysis or under Analysis > select MicroRNA Arrays – RMA + DABG (with quantile normalization).
NOTE: The other option available will be RMA+DABG with NO normalization.
6.
If desired, enter a suffix to be appended to the file name, and then select OK. Note, the summarization method is automatically
included in the file name.
7.
Depending on the number of arrays selected, several minutes may be required for processing. Once processing is complete the
newly summarized data (CHP files) will appear in a new group in the Study window. The title of the new group will be “RMADABG – Group 1”. If other analysis runs have been completed already the group number will be incremented.
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Expression Console™ miRNA Quick Start Guide
8.
Highlighted rows in the Study Table signify CHP files that contain metrics outside of the user defined thresholds. To display to
thresholds there are three options:
 Menu bar: Edit > Report Thresholds
 Toolbar: the button,
 Toolbox: Configuration > (4) Specify Report Thresholds
9. The newly created CHP files are now ready for QC analysis within the Expression Console software or other software provided by
a GeneChip Compatible partner. The CHP files can be found in the same directory as your original input CEL files. The available
views include:
1. View: Report-Full Report
Expression Console™ miRNA Quick Start Guide
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2. View: Report – Transposed
3. View: Probe Level Summarizations
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Expression Console™ miRNA Quick Start Guide
4. Custom Report: New--Report
NOTE: THE DABG values for the controls will show as 0.000 because the values are extremely small and the display in EC cannot
show the values. If you want the exact values, please export the results (pivot table) and you will be able to get the exact p-values for
the Controls.
10. Viewing graphs.
In addition to the tabular display of the metrics, the Expression Console software supports several different graphical views,
including signal histograms, box plots, line graphs, and heat maps depicting the correlation between arrays. The graphical displays,
especially the box plots and heat maps, are useful in identifying outlier samples.
Expression Console™ miRNA Quick Start Guide
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EXAMPLES: Here are some examples of graphs that you can see with miRNA data.
11. Exporting data.
Expression Console provides several options for exporting data:
NOTE: For miRNA data, the Export Report to GCOS RPT File and Export and View GCOS MAS5 Report options are NOT available.
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Expression Console™ miRNA Quick Start Guide
Documentation and support
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For Research Use Only. Not for use in diagnostic procedures.