[BioC] Normalization

[Adaikalavan RAMASAMY]

The Average Difference value you describe is generated by MAS 4.0
algorithm which fairly outdated. The newer algorithm, MAS 5.0, uses
Ideal Mismatch values to force the resulting signal to be very small
positive values. [ Even then there is some evidence this algorithm is
suboptimal ]

Some reference (below) treat any value less than +20 (or any other small
positive number) as unreliable/missing.

If you have the raw experiment files (CEL files), you might be able to
get outputs according to newer algorithms which does not produce
negative values.
http://expression.gnf.org/faq.html#avgdiff
http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v33/n1/full/
ng1061.html

Regards, 

--
Adaikalavan Ramasamy 

-----Original Message-----
From: Kaushik, Narendra K [mailto:n.kaushik at imperial.ac.uk] 
Sent: Wednesday, October 08, 2003 10:23 PM
To: 'bioconductor at stat.math.ethz.ch'
Subject: [BioC] Normalization


I have lots of negative values. What is the best way to get rid of them
or to normalize the data. I am working with Avg_diif values.

Narendra Kaushik
Imperial College of Medicine,
London SW3 6NP
UK

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