[BioC] valcano plot x-values

[sabrina.shao]

James W. MacDonald wrote:

> 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,
>
Hi, Jim:
Thanks a lot for the info. I did get that information from the help 
file, but my question is that what exactly is the x-axis value since it 
is propotional to the FC , not the FC itself. I have 12 arrays from 4 
strains with each having 3 biological replicates. So I am doing the 
F-test instead of pairwise Ttest. Would you please explain it to me? 
Thanks for your help

Sabrina