[Gmod-help] storing average expression data in MAGE module of Chado?

[Allen Day]

Ian,

Try using the quantification_relationship table.  Your subject_id will
be the average, type_id is derives_from (or your own subtype of this),
object_id is used for each of the arrays going into the average.

-Allen

On Tue, Apr 21, 2009 at 8:36 PM, Dave Clements, GMOD Help Desk
<gmodhelp at googlemail.com> wrote:
> Hi Ian,
>
> I am afraid that you may possibly now know more about the MAGE module
> than anyone at the GMOD Help Desk.  I don't believe that any of us
> have ever worked with it.
>
> I'm forwarding your query to Brian O'Connor and Allen Day, whom I
> believe are the two people who contributed the MAGE module to GMOD.
> Brian, Allen, any ideas on Ian's question?
>
> Regards,
>
> Dave C.
>
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>
> Learn more about GMOD at SMBE & Arthropod Genomics:
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>  http://www.k-state.edu/agc/symp2009/seminar.html
>
>
>
> On Tue, Apr 21, 2009 at 2:32 PM, Ian Davis <ian.w.davis at gmail.com> wrote:
>> Hi,
>>
>> I'm trying to set up a Chado database to hold expression data from a
>> bunch of Affymetrix chips, using the MAGE module.  I can see that for
>> a single chip, I should create one new entry in each of "assay",
>> "acquisition", and "quanitification", and for each expression
>> measurement create a new entry in "elementresult".
>>
>> However, we often do multiple replicates of the same experiment, and
>> work from the averaged expression levels.  I can see how to store the
>> individual replicates (as above).  But I can't see how to store the
>> *average* of them.  It seems like I would create a new
>> "quantification" (and associated "elementresult"s) that referred to
>> multiple "acquisition"s, but I can't see a way to do that.
>>
>> Any suggestions?
>>
>> Thanks!
>> Ian
>>
>