[Obi-protocol-application-branch] normalization objective

[Philippe Rocca-Serra]

Hello DT/Plan,

I am about to submit several new terms to PA , one of them, library
normalization seems to requires alteration to the definition of
normalization objective as well as it current location under data
transformation objective.

current definition for 'normalization objective' is: a data
transformation objective where the aim is to remove systematic source of
variation to put the data on equal footing in order to create a common
base for comparison.

The objective pursued during the normalization step when constructing a
cDNA library is closely related, that is to remove very abundant element
in order to allow rarer element to be picked up.

Option1: agree on common definition for normalization objective , that
would sit outside of data transformation objective but of course could
be used to define data transformation
normalizatio objective: an objective specification where the aim is to
remove systematic source of variation in order to create a common based
for comparison
parent class: objective specification

Option2:
i. leave 'normalization objective' where it stands in the current
hierarchy but alter the label to 'data normalization objective'
ii. create a library normalization objective as a child of material
transformation objective with its own definition

Let me know which you prefer or if you can think of another route.

Cheers

Philippe

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[James Malone]

Hi Philippe,

I don't know much about cDNA library normalization - what is the input and
output of a such a cDNA library normalization? If it's not data in and
out, it would suggest they are different enough to separate them out. I'd
be a little concerned about generalising 'normalization' and have types
under this as there are some uses of the word that are not related, e.g.
database normalization. I'd probably go with the latter option (creating
data normalization and library normalization and keeping them apart).

Cheers,

James

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[Philippe Rocca-Serra]

Hi James,

I agree with you that the protocol and data trasnformation should be
different, I was just thinking the objective is somewhat similar, namely
allow comparison.
Writing this up, it seems that the removal of redundancy is absent from
the 'data normalization' (but present in database normalization).
At the end of the day, we'll probably need to refined the objective to
data normalization objective.

thanks for the quick feedback.

P

[James Malone]

FYI name has now been changed in file to data normalization objective.

--
EMBL Outstation - Hinxton,
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD,
United Kingdom
Fax: + 44 (0) 1223 492 468