Dahlquist:GenePix Pro Software Protocol
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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, and the magnifying glass return icon to go back to the whole chip image
- Zoom in so that you can see the entire top block of grids on your screen
- On the right hand side of the screen, select the File icon
- Select Load Array List
- Red, orange, yellow, green, and pink groups, use the file "yeast_GCAT_Fall2006_gal.gal"
- Blue group, use the file "GCAT_384_illumina_Spring2007.gal"
- Click the Open button
- Using the icon that has an arrow and a square, drag the grids so that they are approximately aligned with the top block of spots
- Click on the icon that looks like a compass, or a circle with cross-hairs, and select Find Array
- Click on the icon again, and select Find All Blocks
- Click on the icon again, and select Align Features in All Blocks
- On the right hand side of the screen, select the icon that looks like a table of data (it says B, C, R at the top of it)
- In the Results tab, click on the button to Configure Normalization
- Make sure that "Ratio-based" is selected and it says that the "Ratio of medians" of "all of the features" is equal to "1"
- Click the Normalize button
- Click on the File icon on the right hand side and select, Save Results As, and save your results.
- Repeat this procedure with the bottom block on the slide.
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