hi, i've been trying to get an idea about the implementation of the mas 5 backgound adjustment in the affy package. where it says in the sadd a(x,y) = max( i(x,y)-b(x,y) , nf*n(x,y) ) where i(x,y) = max(i(x,y),0.5) i've just been able to find the first line implemented. where did i miss the second line? or is it not implemented becaus .5 is so small that it should rarely take effect? (if that's the case, which is my guess, why is it in the sadd?) dennis -- Max-Planck-Institute for Molecular Genetics Computational Molecular Biology Ihnestrasse 63-73 D-14195 Berlin -- Tel: ++49 (30) 8413-1178 Fax: ++49 (30) 8413-1152

On Wed, 2003-02-05 at 02:49, Dennis Kostka wrote: > hi, > i've been trying to get an idea about the implementation of the mas 5 > backgound adjustment in the affy package. where it says in the sadd > > a(x,y) = max( i(x,y)-b(x,y) , nf*n(x,y) ) where > i(x,y) = max(i(x,y),0.5) > > i've just been able to find the first line implemented. where did i miss the > second line? or is it not implemented becaus .5 is so small that it should > rarely take effect? Cell intensities that low are extremely rare in my experience. In fact I am not sure I have ever come across one. You'd be able to see if you are getting anywhere near that with your data by looking at the min(pm(....)) and min(mm(....)) where .... is your AffyBatch. > (if that's the case, which is my guess, why is it in the > sadd?) Affymetrix reason for doing things is not always clear. Ben