Dahlquist:GenePix Pro Software Protocol: Difference between revisions
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== Using GenePix Pro == | == Using GenePix Pro == | ||
=== Gridding and Generating Intensity Data === | |||
* Launch GenPix Pro (select Analysis Only) === | |||
* On the right hand side of the screen, select the File icon | |||
** Select File > Open Images | |||
** Navigate to the folder containing your .tif images | |||
** Hold down the Control key while clicking to select both the 532 and 635 wavelength files | |||
** Click on the Open button | |||
* Use the brightness and contrast sliders on the upper left hand side to adjust your image to see all of the spots | |||
* You can use the magnifying glass icon to zoom in on an area of the image | |||
=== Generating an Array Quality Report === | === Generating an Array Quality Report === |
Revision as of 20:34, 13 April 2010
Using GenePix Pro
Gridding and Generating Intensity Data
- Launch GenPix Pro (select Analysis Only) ===
- On the right hand side of the screen, select the File icon
- Select File > Open Images
- Navigate to the folder containing your .tif images
- Hold down the Control key while clicking to select both the 532 and 635 wavelength files
- Click on the Open button
- Use the brightness and contrast sliders on the upper left hand side to adjust your image to see all of the spots
- You can use the magnifying glass icon to zoom in on an area of the image
Generating an Array Quality Report
- Launch GenePix Pro (select Analysis Only)
- On the right hand side of the screen, select the File icon
- File > Open Results
- Select the desired file
- Select Report tab at the top of the screen
- On the left side of the screen, under Navigate, select the back arrow or home icon
- Select Array Quality Control
- Adjust Vital Statistic Thresholds values to:
Quality Control Limits Median signal to background > 2.5 Mean of Median background < 500 Median Signal to Noise > 4 Median % >B + 1 StdDev > 90 Feature variation < 0.5 Background Variation < 1.2 Features with Saturated pixels < 3.3% Not Found < 18% Bad Features < 7%
- Select Start
- Select Show Printable Version
- File > Print
- Under Select Printer > Select Adobe PDF
- Select Print
- Save on the Desktop
- Name the file: Chip #_Year-Month-Date
- The PDF file will either open on its own or you need to open it from the file you saved it to
- Print the first two pages of the results