I have recently installed the Illumina Plugins and have imported  
features for several Array Designs. We modified our config to  
generate the Bead Summary files and I have imported the data. Oddly  
have found that the Bead Summary files contain some rows with  
illumina codes that are not in the BGX files. For example the  
datasets from HumanRef-8 arrays contain 324 probes that are not found  
in any of the various versions of BGX files are available from the  
Illumina web site. If I run these same datasets through BeadStudio  
these these probes are not found in the BeadStudio output.

Has anyone else run into this situation?

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