[BioC] flagged spots in marray

[Juan Pedro Steibel]

Hi all,

I am trying to find out more about the use of flags by the marray 
package. In particular for normalization purposes.

It seems that if I read a set of array files with flags and perform, 
say, loess print tip normalization and then I replace all flags with 
zeroes and repeat the analysis, I am not getting the same results.... 
sometimes quite different.

Note that I have a whole zoo of flags in these data: a good share of 
-50, -75 and -100... a lot of them introduced manually by a human 
operator to mark "visually suspicious" array sectors.

Is there any document that explains the internal use of flags by the 
normalization functions in marray?

Thanks in advance!
Juan Pedro

-- 
=============================
Juan Pedro Steibel
Postdoctoral researcher
Statistical Genetics
Department of Animal Science 
Michigan State University
1205-I Anthony Hall
East Lansing, MI
48823 USA 
Phone: 1-517-353-5102
E-mail: steibelj at msu.edu