[BioC] flagged spots in marray

Juan Pedro Steibel steibelj at msu.edu
Thu May 17 23:32:42 CEST 2007

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

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