[BioC] ComBat: How to choose multiple covariates in ComBat analysis- Need advice

[hu duan]

Hi Dr. Johnson,

I have one question about multiple covariates in ComBat analysis that
bother me for two weeks and I really need your advice.

I have a microarray experiment design list below and please look at
the *attachment
*for details.


   1. I ran experiments in 4 different dates in a randomized way, so 4
   batches.
   2. Each sample has been run with 2 or 3 replicates.
   3. 4 parameters(individual, age, status, stage) associate with each
   sample. None of them is nuisance. Batch is ONLY the effect I want to
   eliminate.

*Analysis I want to do:*

I want to perform statistic test to find significant features between
groups by status first and then see how they behave on different
Individual, stages and ages. I will later select features to distinguish
different stages.

So I need a method to consider individual, age, status, stage at same times
when doing ComBat analysis, so that their biological difference will not be
eliminated.

*My question is:*

What covariates do I need to include? What will be the influence without
including them? Can you mention the principle of choosing multiple
covariates?

Thanks

Tiger

PS:  The bell plot can show batch removed result. But is there a good way
to give a quantitative parameter, such as a percent to show how many batch
effects have been removed? So we can know how ComBat perform and can
convince reviewers?

-- 
Hu Duan (Tiger)
Biological Design PhD student
Graduate Research Associate
Center for Innovation in Medicine
The Biodesign Institute, Arizona State University
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"MY MIND REBELS AT STAGNATION." -- Sherlock Holmes
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-- 
Hu Duan (Tiger)
Biological Design PhD student
Graduate Research Associate
Center for Innovation in Medicine
The Biodesign Institute, Arizona State University
----------------------------------------------------------------------------
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"MY MIND REBELS AT STAGNATION." -- Sherlock Holmes
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