[BioC] SCAN UPC probability - validation of gene expression results using UPC

[Gadi Miron [guest]]

Hello all, 

I currently use SCAN to normalize Affimetrix HGU133A2 arrays, and COMBAT for treatment of batch effect in normalized arrays. I would like to implement the new UPC option - I have questions regarding :

1. From which probability is it safe to assume that feature represents true signal ? Should I cut off at 0.5, or can I only use features marked as 1? Furthermore, should all features with a low probability of being true signal be filtered out of downstream analysis, and should this filter be applied before or after using COMBAT for batch effect correction ?

2.  The expression value that is the output of SCAN - these are normalized log2 values? 

Thank you in advance! 

Gadi Miron
gadi.miron at gmail.com

 -- output of sessionInfo(): 

normalized1 = UPC(celFilePath, "output_file1.txt")

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