[BioC] R/Maanova Tutorial

Juan Pedro Steibel steibelj at msu.edu
Mon Mar 22 17:30:15 CET 2010

Hello Dejian and Ricardo,
I always check the term.levels of the fitmaanova object, where "term" is 
the name of a fixed effects factor in the model.
That should give the name of each level in the order in which they are 
arranged in the incidence matrix X.

Hope this helps

Ricardo Verdugo wrote:
> Dear Dejian:
> Thank you for your message. I admit Maanova lacks some documentation 
> about the constructions of the  contrast matrix, and this point is 
> among the missing items. From my personal experience, I have seen that 
> the columns are in alphabetical order by levels of the terms in the 
> 'term' argument to matest. I usually check the X matrix from the 
> fitmaanova object to make sure. One gets an idea from looking at the 
> coefficients of this matrix.
> If somebody else in the maanova list has any further information about 
> this, please jump in.
> Ricardo.
> On Mar 22, 2010, at 10:51 AM, Dejian Zhao wrote:
>> 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.
>> Dejian
>> 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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Juan Pedro Steibel

Assistant Professor
Statistical Genetics and Genomics

Department of Animal Science & 
Department of Fisheries and Wildlife

Michigan State University
1205-I Anthony Hall
East Lansing, MI
48824 USA 

Phone: 1-517-353-5102
E-mail: steibelj at msu.edu

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