Hi
How does arrayQualityMetrics handle spots that have been flagged as bad, those values that are thus missing? We are using imagene files and we can generate 
maQualityPlots and set a badspotfunction parameter to identify bad spots. This allows us to see on a spatial plot flaged spots as black sqaures.

Do you have any suggestions as what we can do with these flagged values for use in arrayQualityMetrics? How does arrayQualityMetrics handle missing values?
regards
Louise


      
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