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h1. |
Problem:
...
How
...
do
...
I
...
take
...
advantage
...
of
...
the
...
new
...
Agilent
...
Custom
...
2
...
x
...
415K
...
human
...
CGH
...
platform
...
supported
...
in
...
v1.3.1?
...
Topic:
...
caIntegrator
...
Usage
...
Release:
...
caIntegrator
...
v1.31
...
and
...
above
...
Date
...
entered:
...
01/10/2012
...
Solution
As of v1.3.1,
...
caIntegrator
...
supports
...
a
...
new
...
in
...
situ
...
oligonucleotide
...
array
...
platform
...
known
...
as
...
Agilent
...
Custom
...
2
...
x
...
415K
...
Human
...
CGH
...
(Comparative
...
Genomic
...
Hybridization),
...
which
...
is
...
an
...
update
...
of
...
the
...
stock
...
Agilent
...
SurePrint
...
G3
...
Human
...
CGH
...
Microarray
...
Kit
...
2x400K
...
platform
...
(catalog
...
no.
...
G4448A)
...
adapted
...
by
...
The
...
Cancer
...
Genome
...
Atlas
...
(TCGA)
...
project.
...
 For
...
detailed
...
technical
...
specifications
...
of
...
the
...
platform,
...
please
...
refer
...
to
...
...
...
on
...
the
...
NCBI
...
site.
...
This
...
newly
...
supported
...
platform
...
is
...
similar
...
to
...
others
...
in
...
that
...
it
...
generates
...
copy
...
number
...
results
...
as
...
a
...
data
...
type.
...
Unlike
...
SNP-based
...
platforms,
...
however,
...
Agilent
...
Custom
...
2
...
x
...
415K
...
Human
...
CGH
...
does
...
not
...
generate
...
LOH
...
(Loss
...
of
...
Heterozygosity)
...
or
...
SNP
...
(Single
...
Nucleotide
...
Polymorphism)
...
data.
...
For
...
more
...
information
...
about
...
how
...
Agilent
...
Custom
...
2
...
x
...
415K
...
Human
...
CGH
...
compares
...
to
...
other
...
array
...
platforms,
...
please
...
refer
...
to
...
...
...
on
...
the
...
TCGA
...
wiki.
...
Please
...
note
...
that
...
the
...
platform's
...
design
...
file
...
does
...
not
...
come
...
bundled
...
with
...
the
...
caIntegrator
...
installer;
...
it
...
must
...
be
...
downloaded
...
separately
...
and
...
manually
...
loaded
...
into
...
the
...
application
...
by
...
the
...
study
...
manager
...
or
...
other
...
end
...
user.
...
The
...
design
...
file
...
is
...
attached
...
to
...
this
...
message
...
and
...
can
...
be
...
downloaded
...
in
...
ADF
...
format
...
at
...
the
...
following
...
link:
GPL13346_family_all_reporters_tdt.adf
...
Please
...
also
...
note
...
that
...
design
...
files
...
download
...
from
...
Agilent
...
or
...
other
...
sites
...
may
...
not
...
work
...
in
...
caIntegratpr,
...
as
...
they
...
may
...
need
...
to
...
have
...
their
...
headers
...
modified
...
before
...
being
...
loaded
...
into
...
the
...
application.
...
The
...
ADF
...
file
...
attached
...
to
...
this
...
message
...
has
...
already
...
been
...
modified
...
to
...
work
...
in
...
caIntegrator.
...
Have
...
a
...
comment?
...
Please
...
leave
...
your
...
comment
...
in
...
the
...
...
...
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Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=23&t=461].
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