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