[BioC] 2-way Anova analysis

James W. MacDonald jmacdon at med.umich.edu
Fri Jan 6 15:26:01 CET 2006

Sharon wrote:
> Hi Donglei & James
> Thanks for your reply.  I am sorry for not making myself clear. I already
> have this matrix that contains Probeset    p-value (strain effect) p-value
> (treatment effect) p-value (interaction).  As you suggested, I can use
> pvalue cut-off to select probesets for strain effect. From the selected list
> (for strain effect), I would like to choose probsets that are significant
> for Strain A and then for Strain B.  In the same way, I would like to select
> probesets for Treatment A and Treatment B.

I think you might be misunderstanding what significance means in this 
context. If there is a significant strain effect for a particular 
probeset (assuming there isn't a significant interaction term for that 
probeset), this simply means that there is a significant _difference_ 
between the two strains for that probeset. Therefore you cannot 
attribute significance to either strain since it is the difference in 
expression that is significant.



> I hope, this explains my problem.
> Thanks again,
> Sharon

James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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