[BioC] R/Maanova Tutorial

Dejian Zhao zhaodj at ioz.ac.cn
Mon Mar 22 15:51:08 CET 2010

 Thank you for your detailed tutorial, Ricardo. It is a great help to me, 
but there is still something confusing me. It is about the contrast matrix.

Simply speaking, I don't know how to decide the meanings of the columns 
in the contrast matrix. You ASSUME the experimental groups are stored 
alphabetically (line 199 in YChrom-DE.R), and then construct the 
contrast matrix. Are they truely stored in this way? It confused me at 
this point when I deal with my own data, because I don't know how my 
data is stored. Can you provide a way to decide the actual order of 
storage? It will help me build the contrast matrix.

Thanks a lot.


Ricardo Verdugo wrote:
> Hello:
> I am at Gary Churchill's group where R/MAanova is developed and  
> maintained. After assisting numerous users with similar issues, I  
> though it would be better to write a self contained tutorial that  
> would walk newbies through a differential expression analysis using  
> contrasts.
> You can get the tutorial (data included) and see the expected results at
> http://churchill.jax.org/software/rmaanova/tutorials.shtml
> It is well documented, explained step by step.
> This is work in progress so comments are welcome. If other tutorials  
> would be useful, send an email to maanova at jax.org
> Regards,
> Ricardo Verdugo
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Ricardo A. Verdugo S., D.V.M. Ph.D.
> Postdoctoral Fellow
> Gary Churchill Group
> The Jackson Laboratory
> 600 Main Street,
> Bar Harbor, ME 04609
> ricardo.verdugo at jax.org
> +1-207-288-6715
> +1-207-288-6847 Fax
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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