Dahlquist:GenePix Pro Software Protocol: Difference between revisions

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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 ==
=== 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

Revision as of 20:38, 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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