[BioC] 2 color data...

milesg at bu.edu milesg at bu.edu
Tue Jul 18 17:48:37 CEST 2006

HI, my name is Gregory Miles. I'm at Boston University and was given this 
address by Dr. Carey (I went to a seminar of his last week) at the Harvard 
medical school and was told that I could ask my question about 2 color data to 
you. On the mouse microarray dataset we have, there are two colors, and 
therefore two values that can be below background. When both values are above 
background (zero_barcode on our chip), we keep the data and when both are 
below we eliminate the data (they become NA). I imagine this is a correct 
approach, but what should be done regarding the data that has one intensity 
below background and one above. Would it be best to keep the good value? Do we 
eliminate the entire gene from entry into bioconductor? Perhaps there is a way 
to specify to bioconductor that this is the case (by entering a background 
value) and allowing it to handle the data abstractly? Or is it best to let 
Bioconductor look at them as NA's. Any help would be greatly appreciated. 
-Greg Miles

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