[BioC] flagged spots in marray

Juan Pedro Steibel steibelj at msu.edu
Fri May 18 03:41:19 CEST 2007

Hello again,
I already figured out a problem in my script and realized that (by 
default) the flags are being ignored by the normalization routines.
Please, disregard my previous email.


Juan Pedro Steibel wrote:
> 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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