Hi list

 

I am working on a data set from 24 arrays, where each array consist of
6.912 spots replicated pair wise at two different spatial locations.

For quality evaluation, I have calculated the CV of "raw" log-ratios for
each pair wise replicated spot (13.824 points per array) and have
observed the expected tendency of decreasing CV by increasing average
spot intensity.

When calculating the CV for normalized data, I have observed that the CV
has increased compared to CV for raw data. This essentially means that
normalization is making data worse in terms of variance among replicated
spots!

 

Has anybody observed something similar?

Is this what should be expected or does it indicate that the
normalization is not optimally performed?

 

Looking forward hearing from you!

Jakob

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Jakob Hedegaard

Danish Institute of Agricultural Sciences

Department of Genetics and Biotechnology

Molecular Genetics and System Biology

Building K25

Research Centre Foulum

P.O. box 50

DK-8830 Tjele

Denmark

Tel: (+45)89991363

Fax: (+45)89991300

 


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