Dahlquist:GenePix Pro Software Protocol

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