Prior to using SCAN.UPC and ComBat, we originally ran NUSE (in AffyPLM) and
removed Affy Hu-133A arrays for which the NUSE criterion was > 1.05.   We
are wondering whether use of SCAN.UPC without pre-filtering by NUSE would be
sufficient?  Also, regarding artifacts and degraded hybridization regions on
chips (visible in AffyPLM Residual plots in the form of streaks, blotches,
hot spots, etc.),  we are wondering what SCAN.UPC would do with such
perturbations?  

 

Leif Peterson

HMRI, Houston 


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