[BioC] valcano plot x-values

[James W. MacDonald]

Hi Sabrina,


> 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? 

Ah, that is a different question. For a 100% accurate response, you 
should contact Hao Wu (hao at jax.org) who wrote the maanova package.

However, from poking around in the code, it appears that the x-axis will 
be the fold change if you are doing a t-test, and it will be the 
'average fold change' if you are doing the F-test. I say 'average fold 
change' because it is really the square root of the sums of squared 
differences. This is because the F-test is testing for a difference 
between any sample, regardless of direction, so you square the 
differences first to make everything positive. This is why the volcano 
plot for the F-test only has positive 'fold changes'.

In the case of the F-test the x-axis doesn't really have much meaning 
because it is a combination of all the comparisons.

HTH,

Jim




> Thanks for your help
> 
> Sabrina
> 


-- 
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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