[BioC] R/Maanova Tutorial

Ricardo Verdugo ricardo.verdugo at jax.org
Mon Mar 22 16:08:57 CET 2010

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.


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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