Illumina Resources

Data sets

• Example bead level data used in beadarray vignette [BeadLevelExample.zip]
• Example bead summary data used in beadarray vignette [BeadSummaryExample.zip]
• Example bead level data used in BioC07 practical [SAMExample.zip]

Scanner Settings

Follow the steps below to obtain bead level data for Illumina arrays. You will need to modify the settings for BeadScan before scanning an array - there is no way to retrieve the bead level data after the array has been scanned.

The following .xml files contain the appropriate settings for BeadScan (works on version 3.1 or later only for X, Y bead locations):

• Settings for obtaining bead level data (i.e. probe level codes and X and Y bead locations) [SettingsBeadLevel.xml].
• Settings for NO bead level data from BeadScan [SettingsNObeadlevel.xml]

Instructions for changing settings on BeadScan :

• Download the appropriate xml file (above)
• Browse to C:\Program Files\Illumina\BeadScan
• Find the file Settings.xml (the current settings file used by BeadScan). Rename this file as SettingsOriginal.xml
• Save the file SettingsBeadLevel.xml as Settings.xml in the same directory (C:\Program Files\Illumina\BeadScan). Then restart the BeadScan software; column headings of output files from BeadScan will be Code, Grn, GrnX, GrnY.
• To disable bead level output from BeadScan, replace Settings.xml with SettingsOriginal.xml in the C:\Program Files\Illumina\BeadScan directory. Then restart the BeadScan software.

Many thanks to Matthew Forrest (Sanger Institute, UK) for these instructions and xml files.