Dahlquist:GenePix Pro Software Protocol

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(Using GenePix Pro: pasted in from Olivia's Adjusting Threshold Value protocol)
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== Using GenePix Pro ==
== Using GenePix Pro ==
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=== Generating an Array Quality Report ===
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* Launch GenePix Pro (select Analysis Only)
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* On the right hand side of the screen, select the File icon
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* File > Open Results
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* Select the desired file
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* Select Report tab at the top of the screen
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* On the left side of the screen, under Navigate, select the back arrow or home icon
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* Select Array Quality Control
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* Adjust Vital Statistic Thresholds values to:
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Quality Control Limits Value
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Median signal to background > 2.5
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Mean of Median background < 500
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Median Signal to Noise > 4
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Median % >B + 1 StdDev > 90
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Feature variation < 0.5
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Background Variation < 1.2
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Features with Saturated pixels < 3.3%
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Not Found < 18%
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Bad Features < 7%
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* Select Start
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* Select Show Printable Version
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* File > Print
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* Under Select Printer > Select Adobe PDF
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* Select Print
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* Save on the Desktop
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* Name the file: Chip #_Year-Month-Date
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* The PDF file will either open on its own or you need to open it from the file you saved it to
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* Print the first two pages of the results

Revision as of 23:38, 12 April 2010

Using GenePix Pro

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	Value
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
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