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Question: How do I export experiment annotation and data file into MAGE-TAB and GEO SOFT formats?
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Topic: caArray Usage
Release: caArray
...
2.3.1
...
and
...
later
...
Date
...
entered:
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5/20/2010
...
Answer
caArray Download Options
Starting with caArray 2.3,
...
the
...
Export
...
Experiment
...
Annotation
...
Packages
...
option
...
in
...
caArray
...
allows
...
users
...
to
...
export
...
the
...
experiment
...
annotations
...
(and
...
optionally
...
data)
...
into
...
MAGE-TAB
...
format
...
and
...
GEO
...
SOFT
...
format
...
for
...
GEO
...
submission.
...
Export
...
Experiment
...
Annotation
...
Packages
...
under
...
Data,
...
Download
...
Data
Exporting to MAGE-TAB
The user can generate MAGE-TAB files that consolidate the related annotation information about the experiment in the caArray repository.
To perform this task, click the MAGE-TAB (Annotations Only) link.
Links to Select an Option to Export Experiment Annotation Packages
The MAGE-TAB generated is a live export of the current state of the experiment's annotations, capturing all previous changes made via MAGE-TAB import and/or the Annotations GUI.
This process will generate an IDF and a SDRF file containing information about the experiment including biomaterial-hybridization-data chains, biomaterial characteristics and material type, source providers, labeled extract labels, experiment title and description, and term source (vocabulary) information. Export of other attributes like experimental factors, protocols, publications, persons, etc. is deferred.
Exporting to GEO SOFT
The export to GEO SOFT option allows the user to generate a data package that will meet the requirement for GEO SOFT submission. This option is currently available only for Affymetrix experiments in caArray v.2.3.1.
...
There
...
are
...
two
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options
...
to
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export
...
to
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GEO
...
SOFT:
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Option
...
1.
...
Annotation
...
file
...
only
...
caArray
...
validates
...
that
...
all
...
the
...
mandatory
...
annotations
...
are
...
present,
...
translates
...
the
...
experiment
...
annotations
...
into
...
GEO
...
SOFT
...
format
...
and
...
prompts
...
users
...
to
...
save
...
the
...
generated
...
.soft.txt
...
file
...
(see
...
Arrow
...
2
...
in
...
Figure
...
2
...
).
...
Option
...
2.
...
GEO
...
SOFT
...
submission
...
package
...
This
...
option
...
allows
...
the
...
user
...
to
...
export
...
both
...
annotation
...
files
...
and
...
data
...
files.
...
caArray
...
first
...
validates
...
that
...
all
...
the
...
mandatory
...
annotations
...
are
...
present,
...
then
...
translates
...
the
...
experiment
...
annotations
...
into
...
GEO
...
SOFT
...
format
...
and
...
prompts
...
users
...
to
...
save
...
an
...
archive
...
containing
...
the
...
.soft.txt
...
file,
...
and
...
all
...
raw,
...
derived
...
and
...
supplementary
...
files
...
(see
...
Arrow
...
3
...
in
...
Figure
...
2
...
).
...
If
...
the
...
archive
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is
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less
...
than
...
2
...
GB,
...
the
...
package
...
is
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provided
...
in
...
the
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.zip
...
format;
...
otherwise,
...
it
...
is
...
provided
...
in
...
tar.gz
...
format.
...
This
...
export
...
option
...
is
...
available
...
only
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for
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the
...
experiments
...
whose
...
annotation
...
and
...
data
...
files
...
were
...
uploaded
...
with
...
MAGE-TAB
...
format.
...
Requirement
...
for
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Exporting
...
to
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GEO
...
Soft
...
Before
...
launching
...
the
...
GEO
...
SOFT
...
Export,
...
caArray
...
will
...
validate
...
the
...
experiments
...
and
...
make
...
sure
...
the
...
following
...
requirements
...
are
...
met:
...
- The
...
- experiment
...
- must
...
- have
...
- at
...
- least
...
- one
...
- array
...
- design.
...
- The
...
- provider
...
- for
...
- the
...
- array
...
- designs
...
- must
...
- be
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- Affymetrix.
...
- All
...
- array
...
- designs
...
- associated
...
- with
...
- the
...
- experiment
...
- must
...
- be
...
- ones
...
- for
...
- which
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- caArray
...
- has
...
- the
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- GEO
...
- accession.
...
- Every
...
- hybridization
...
- must
...
- have
...
- at
...
- least
...
- one
...
- raw
...
- data
...
- file.
...
- Every
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- hybridization
...
- must
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- have
...
- a
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- derived
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- data
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- file
...
- of
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- type
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- AFFYMETRIX_CHP.
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- The
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- following
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- protocols
...
- must
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- be
...
- present:
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- extract,
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- label,
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- hybridization,
...
- scan
...
- and
...
- data
...
- processing.
...
- (These
...
- are
...
- entered
...
- via
...
- MAGE-TAB.)
...
- There
...
- must
...
- be
...
- at
...
- least
...
- one
...
- characteristic
...
- or
...
- factor
...
- value
...
- that
...
- is
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- present
...
- for
...
- every
...
- hybridization
...
- somewhere
...
- in
...
- its
...
- biomaterial
...
- chain.
...
- For
...
- every
...
- biomaterial
...
- chain,
...
- the
...
- Material
...
- Type
...
- of
...
- the
...
- extract
...
- or
...
- labeled
...
- extract
...
- must
...
- be
...
- present.
...
- For
...
- every
...
- biomaterial
...
- chain,
...
- the
...
- label
...
- of
...
- the
...
- labeled
...
- extract
...
- must
...
- have
...
- a
...
- non-empty,
...
- non-null
...
- value.
...
- caArray
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- informs
...
- the
...
- user
...
- of
...
- the
...
- result
...
- of
...
- the
...
- validation,
...
- and
...
- provides
...
- the
...
- list
...
- of
...
- errors
...
- if
...
- the
...
- validation
...
- did
...
- not
...
- succeed.
...
Samples
...
of
...
MAGE-TAB
...
Template
...
Only
...
the
...
experiments
...
entered
...
into
...
caArray
...
via
...
MAGE-TAB
...
file
...
upload
...
are
...
eligible
...
for
...
GEO
...
SOFT
...
Export.
...
Various
...
knowledge
...
base
...
entries
...
(refer
...
to
...
...
...
...
...
...
)
...
have
...
been
...
created
...
explaining
...
MAGE-TAB
...
format
...
files
...
and
...
how
...
to
...
upload
...
MAGE-TAB
...
them.
...
A
...
sample
...
package,
...
including
...
datafiles
...
and
...
MAGE-TAB
...
annotation
...
files
...
(.idf
...
and
...
.sdrf
...
files),
...
can
...
be
...
downloaded
...
below
...
to
...
help
...
the
...
user
...
get
...
a
...
quick
...
start:
...
templates
...
for
...
...
...
...
...
...
.
An adventurous user may also download MAGE-TAB annotation files directly from caArray as explained in this article.
Have a comment?
Please leave your comment in the caArray End User Forum.
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