[BioC] ttest or fold change

[A.J. Rossini]

"Jason Hipp" <jhipp at wfubmc.edu> writes:

> I am comparinga relatively homogeneous cell culture to another that has been treated, and am using RMA.  
>  
> I only have 3 replicates of each.  Would you recommend a 2 tailed equal variance t test?  
> I also thought I read that with such few replicates, a fold change would be better than a t test?
> If I get a t test of .0001, and a fold change of 1.2, is this a reliable change using RMA?

You need to consider:

1. what is that value compared to the others from the experiment
2. are you doing an exploratory analysis to be confirmed later or is
   this part of the final scientific justification?
3. you can't treat it like a black box.  Context-free science is
   pretty much content-free (i.e. what cell culture, what treatment,
   apriori should the differences be large, etc.. etc...)

If you are just generating hypotheses, probably reasonable, based on
MY ASSUMPTIONS.  Of course, you are probably violating those, since
I'm not telling you what they are and you have no clue as to whether
I'm reasonable or insane this morning.  

(think about that for a bit and re-read what you wrote... how can we
know what you've done from the above?  how can you even come close to
justifying equal variance?  Are you just looking for a way to order
the results?)

best,
-tony

-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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