Quick Reference Card
Expression Console™
The purpose of the Expression Console™ software application is to enable probe set summarization and initial data quality examination
for GeneChipTM 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
Transcriptome Analysis Console Software, or software applications from GeneChip-compatible™ partners like PartekTM Genomics Suite™
and SpotfireTM.
Quick Start Procedure
1. Download the necessary library files for analyzing your array type if they are not already in the library file directory.
a.
b.
c.
Go to the File menu and select Download Library Files.
Enter your NetAffxTM email address and password.
NOTE: If you have not previously registered, you need to register at our web site.
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. You can 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 Thermo Fisher Study window is created.
3. Use the Add Intensity Files button at the bottom of the Thermo Fisher Study window or click Add Intensity Files in the toolbox to
add your collection of CEL files to the Study.
Expression Console™
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 Menu.
6. Select analysis type to perform.
NOTE: You will be provided with multiple analysis work flow options. The default (recommended) analysis work-flow is presented at
the top of the list of available analyses in the drop down menu for your array type. For information on for available analysis options
please refer to the Expression Console Software User Guide available under the Help menu.
7. 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.
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8. 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 the name of
analysis work-flow chosen followed by a group number (e.g., RMA-DABG-Group 1”). If other analysis runs have been completed
already the group number will be incremented.
9. Highlighted rows in the Thermo Fisher 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
10. 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:
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a. View: Report - Full Report
b. View: Report - Transposed
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Expression Console™
c. View: Probe Level Summarizations
d. 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.
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11. 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.
EXAMPLES: Here are some examples of graphs that you can see with miRNA data.
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Expression Console™
12. 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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How to Export Signal Values with Annotation Information
The purpose of the Expression Console™ software application is to enable probe set summarization and initial data quality examination
for gene expression arrays. To aid in the analysis of expression data, a probe level summarization file can be generated by combining
annotation information (contained in comma-separated files (CSV files)) with the signal values into a single tab-delimited file. This probe
level summarization file can then be further analyzed using software applications from GeneChip Compatible partners to identify
differentially expressed genes (www.ThermoFisher.com).
Merging annotation information into a probe set results table is a one step process after a short setup procedure. The setup procedure
consists of two steps: Step 1, download the annotation file corresponding to the array type being analyzed; Step 2, create an annotation
merge file by selecting the annotation information of interest. To merge the annotations with the probe set results, simply open a study
containing the CHP files of interest and select Export > Export Probe Set Results (pivot table) with Annotations to TXT and use the dialog
box to select the appropriate annotation merge file.
Set-up
1.
Download the necessary annotation files for the array type if they are not already in the library file directory.
a.
b.
c.
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From the File menu and select Download Annotation Files.
Enter your NetAffx email address and password.
In the NetAffx Annotation File window, check all probe array types that you will be analyzing now or in the future and click the
Download button. You can come back and add more annotation files at a later date.
Expression Console™
2. Create an annotation merge file containing the fields from the CSV file you want to have available in the exported probe set results
file.
a.
From the Edit menu, select Create Annotation Merge File and then select one of the types of annotation merge file to create.




For 3’ Expression arrays, select Create 3’ Expression Merge File
For Gene or transcript level analysis from the Exon and Gene Arrays, select Create Gene Level Merge File
For Exon level analysis, select Create Exon Level Merge File
To use your own comma-separated annotation file, select Create Custom Merge File. Note: the first column of the custom
CSV file must contain the probe set identifiers to be used to match-up the records during the merge.
b. Select the annotation file from the drop-down list at the top of the dialog box.
c. Select the level of the annotations to be used in the merge file. (This is only supported for Thermo Fisher Supplied Annotation
files).
 Top Assignment: Annotations will be based on the single transcript to which the probe set best aligns. Selecting this option
results in a single value for the annotation fields at the expense of information.
 All assignments: The annotation will be based on all of the transcripts contained in the annotation file.
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d. Select the annotation fields of interest.
 Bold indicates the default selections (This is only supported for Thermo Fisher Supplied Annotation files).
 The selected fields each appear in their own column in the probe set summarization results table.
e. Select Save to save the annotation merge file.
f. Enter a name for the annotation merge file when prompted. The name of the CSV file used to create the merge file will
automatically be appended to the name you enter.
g. Depending on the size of the CSV file and the number of probe sets in the file several minutes may be required for processing.
Once processing is complete the newly created annotation merge file is available by selecting Export > Export Probe Set Results
(pivot table) with Annotations to TXT.
Merging Annotation
NOTE: This functionality is only enabled if a study containing CHP files is open.
1. Select Export > Export Probe Set Results (pivot table) with Annotations to TXT.
2. Browse to select the Annotation Merge File Name to use for each group of CHP files by selecting the
button.
3. Select the output folder and enter a name for the file. If files from more than one group are selected the group number will be appended
to the name entered.
4. Select OK.
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Expression Console™
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23 January 2017