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

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