Tech Notes
Q. How can I view the channels of my two-color data side-by-side in GeneSpring?
A. If you wish to compare your two channels (e.g. Cy3 and Cy5) side-by-side in the Graph view, you would need to import your two-color data as one-color files, as follows:
- Select "Import Data" from the File menu. Browse for one of your data files.
- Select to import the file as "custom". Click "Next".
- In the Column Editor, assign both Cy5 and Cy3 data columns as "Signal". Assign other columns, such as "Gene Identifier", and click "Next".
- Select your other data files and finish importing your data.
When importing your files as one-color data, GeneSpring will consider each channel as one separate data file. Create a new parameter called "Channel" or "Dye" in the "Experiment Parameters" option (found under the Experiment menu), and specify which 'file' corresponds to what channel. Set the new parameter as "Continuous" under the "Experiment Interpretation" option. Set the other parameters as "Do Not Display" and click "Save". Now you should see the two channels side-by-side in the Graph view.
It is also possible to view one channel plotted against the other in the Scatter Plot view. In this case, the control channel value (e.g. Cy3) for each gene will be plotted against the signal channel value (e.g. Cy5) for the first sample of your experiment. You may select other samples by changing the "Display Options" of the Scatter Plot view (see tech note on Scatter Plot view Display Options for details).
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