When to use Mean Center/Autoscale?

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When to use Mean Center/Autoscale?

Postby ongwaik » Tue Mar 31, 2009 1:14 pm

I am still confused between Mean Centering and Autoscaling of data. I have read the instruction manual but I am still not very clear about the difference between the two and how should I choose between the two?

Ong
Eppendorf Asia Pacific
ongwaik
 
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Re: When to use Mean Center/Autoscale?

Postby Anders Bergkvist » Tue Mar 31, 2009 3:05 pm

Hi Ong,

Mean center removes offsets between expression profiles. This is useful when comparing samples.

Autoscale does what mean center does and then it also normalize each expression profile with respect to the overall variability of the expression profile. This is useful when comparing genes.

For example, we looked at expression of many genes during the developmental stages of the Xenopus frog. Genes that correlate display similar expression profiles, but possibly at different amplitude. In this case we use autoscaling because the amplitude is not important for our conclusions.

In another example we look at the expression of cancer-related genes in response to different drug treaments. We may expect a dose-dependence and differences in effect between different drugs so when analyzing the samples we use mean center to remove offsets, but maintain the amplitude information.

Best wishes,
Anders
Anders Bergkvist
 
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