[BioC] valcano plot x-values

[James W. MacDonald]

Hi Sabrina,


sabrina.shao wrote:
> Hello:
> I am new to maanova package. Just wonder what is the x values in volcano 
> plot. Is it the relative fold changes of my test vs. control? If it is 
> not, how can I use volcano plot with the relative fold change as the 
> x-axis value. Thanks

Yes. From the help for volcano()

Details:

      This function allows one to visualize the results from the F or T
      tests. The figure looks like an erupting volcano. There will be
      one plot For F-test result and multiple plots for T-test result,
      each plot crresponds to one T-test. You must have F1 test result
      in the input object in order to do volcano plot.

      On the plot, the y-axis value is -log10(P-value) for the F1 test.
      The x-axis value is propotional to the fold changes.

HTH,

Jim
> 
> Sabrina
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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