[BioC] siggenes and log

[James W. MacDonald]

Ashley Lin wrote:
> Hi,
> 
> I probably have a stupid question, but how do I specify that my data is 
> in log in siggenes? I know in the window version of SAM, one can check 
> if the data is in log scale or not, what about in siggenes? is log scale 
> the default?

You don't need to explicitly specify that your data are log transformed 
(although they should be). The reason for this checkbox in SAM is simply 
  for the calculation of fold change, which is done on the normal scale, 
so SAM needs to know if the data need to be unlogged or not.

Jim


> 
> Thanks
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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