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h1. |
Question:
...
Where
...
are
...
the
...
Array
...
Design
...
Files
...
for
...
caArray?
...
Topic
...
:
...
caArray
...
Usage
...
Release
...
:
...
Up
...
to
...
caArray
...
2.X
...
Date
...
entered
...
:
...
02/20/2009
...
Answer
New Feature in caArray 2.3
...
and
...
Up
...
Starting
...
in
...
caArray
...
2.3
...
and
...
up,
...
users
...
can
...
download
...
any
...
array
...
design
...
file
...
stored
...
NCI's
...
public
...
caArray
...
instance.
...
Simply
...
locate
...
the
...
array
...
design
...
file
...
of
...
interest
...
in
...
caArray
...
and
...
launch
...
the
...
download
...
process.
...
Finding
...
Array
...
Design
...
Files
...
No
...
array
...
design
...
information
...
is
...
present
...
with
...
a
...
new
...
caArray
...
installation.
...
This
...
feature
...
provides
...
the
...
flexibility
...
for
...
an
...
organization
...
to
...
upload
...
only
...
the
...
designs
...
they
...
use.
...
This
...
reduces
...
the
...
overhead
...
introduced
...
by
...
loading
...
unnecessary
...
designs,
...
which
...
are
...
often
...
of
...
significant
...
size
...
(100's
...
of
...
megabytes
...
or
...
more).
...
This
...
does
...
mean,
...
however,
...
that
...
users
...
must
...
find
...
and
...
upload
...
all
...
the
...
necessary
...
array
...
design
...
files
...
into
...
their
...
caArray
...
server.
...
Searching
...
for
...
the
...
array
...
design
...
files
...
could
...
be
...
confusing
...
and
...
time
...
consuming.
...
It
...
is
...
possible,
...
if
...
you
...
are
...
not
...
using
...
a
...
new
...
instance
...
of
...
caArray,
...
that
...
the
...
array
...
design
...
file
...
you
...
need
...
already
...
exists
...
in
...
caArray.
...
For
...
example,
...
many
...
array
...
design
...
files
...
have
...
been
...
uploaded
...
into
...
...
...
by
...
the
...
users,
...
and
...
they
...
can
...
be
...
reused
...
for
...
other
...
experiments
...
on
...
the
...
same
...
server.
...
The
...
array
...
design
...
files,
...
unlike
...
other
...
array
...
data
...
files
...
however,
...
are
...
not
...
portable
...
in
...
caArray.
...
That
...
is,
...
they
...
cannot
...
be
...
downloaded
...
from
...
one
...
caArray
...
instance
...
and
...
uploaded
...
to
...
a
...
different
...
caArray
...
instance.
...
The
...
purpose
...
of
...
this
...
knowledge
...
base
...
entry
...
is
...
to
...
consolidate
...
information
...
in
...
one
...
convenient
...
place
...
about
...
the
...
location
...
of
...
array
...
design
...
files
...
from
...
different
...
vendors.
...
The
...
list
...
below
...
is
...
not
...
yet
...
complete.
...
Contributions
...
from
...
the
...
caArray
...
user
...
community
...
are
...
highly
...
appreciated.
...
Please
...
post
...
any
...
links
...
or
...
suggestions
...
in
...
the
...
...
...
...
Array Design Files
Array Provider | Array Design File | Comments | File Location | Supported by caArray? |
|---|---|---|---|---|
Affymetrix | .CDF, .PGF, .CLF | Free Registration is required to download array design .Zip file. After downloading the selected package, one needs to drill down to find the folder containing the .CDF file. | Yes, Parsed | |
GenePix | .GAL | The GenePix array design file needs to be created by the user. The link provided the details of the GenePix array design file format, as well as the instructions to create one. | Yes, Parsed | |
Illumina | .CSV | Illumina's arrays are whole-genome arrays. the BGX version of the array design files for Illumina is yet to be supported by caArray. Please use the text version instead. | Yes / Parsed | |
Agilent | .CSV/.XML, .GAL | The array design file can be pulled out from Agilent's website based the barcode on the array chip. For example, barcode 251643612131 is on the array chip for one of your experiment. You can submit the barcode 251643612131 in the "Array Barcode Submission Form" (the 2nd link on the right), which will then return the array design file for Human miRNA Microarray (G4470A). Agilient also provides array design files in .GAL format, which are created with GenePix's scanner service. To upload these Agilent's .GAL files, please select GenePix's .GAL as the uploading template. | No, Imported but Not Parsed | |
ImaGene | .TPL | N/A, Contribution Appreciated. | No, Uploaded but Not Parsed | |
Nimblegen (Roche) | .NDF | N/A, Contribution Appreciated. | – | No, Uploaded but Not Parsed |
ScanArray | – | N/A, Contribution Appreciated. | – | No, Uploaded but Not Parsed |
UCSF Spot | .SPT | N/A, Contribution Appreciated. | – | No, Uploaded but Not Parsed |
MAGE-TAB | .ADF | Need to create | No, Uploaded but Not Parsed |
| Tip | ||
|---|---|---|
| ||
Before you submit your new array design file for uploading, make sure that you have selected the correct file format from File Format drop down list. The default selection of 'Automatic' from File Format might fail in recognizing some file types. |
Further Readings on Uploading Array Design Files into caArray
- Importing an Array Design into caArray
- Import Array Designs Use Case Specification
- Check Existing Array Design Files on caArray
- Managing Array Designs
Useful Tools
Spotter file to ADF Converter. This converter tool can convert .GAL design file for Biorobotics, Genetix, Agilent, Clontech, Virtek to MAGE-TAB formatted Array Design File (ADF).
Have a comment?
Please leave your comment in the caArray End User Forum.
| Wiki Markup |
|---|
|https://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=6&t=177].
*Array Design Files*
|| Array Provider || Array Design File || Comments || File Location|| Supported by caArray? ||
| Affymetrix | .CDF, .PGF, .CLF | Free Registration is required to download array design .Zip file. After downloading the selected package, one needs to drill down to find the folder containing the .CDF file. | * [Affymetrix Design Library|http://www.affymetrix.com/support/technical/libraryfilesmain.affx] | Yes, Parsed |
| GenePix | .GAL | The GenePix array design file needs to be created by the user. The link provided the details of the GenePix array design file format, as well as the instructions to create one. | * [GAL Format|http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gal]
* [Making GAL Files|http://robinsonlab.stanford.edu/microarrays/gal/docs/Making_GAL_Files.pdf] | Yes, Parsed |
| Illumina | .CSV | Illumina's arrays are whole-genome arrays. the BGX version of the array design files for Illumina is yet to be supported by caArray. Please use the text version instead. | * [Whole Genome Design Files|http://www.switchtoi.com/annotationfiles.ilmn] | Yes / Parsed |
| Agilent | .CSV/.XML, .GAL | The array design file can be pulled out from Agilent's website based the barcode on the array chip. For example, barcode 251643612131 is on the array chip for one of your experiment. You can submit the barcode 251643612131 in the "Array Barcode Submission Form" (the 2nd link on the right), which will then return the array design file for Human miRNA Microarray (G4470A). Agilient also provides array design files in .GAL format, which are created with GenePix's scanner service. To upload these Agilent's .GAL files, please select GenePix's .GAL as the uploading template. | * [Available Design Files|http://www.chem.agilent.com/cag/bsp/array_list.asp]
* [Array Barcode Submission Form|http://www.chem.agilent.com/cag/bsp/pp4_1.asp] | No, Imported but Not Parsed |
| ImaGene | .TPL | N/A, Contribution Appreciated. | [Imagene User Guide|http://signal.biosi.cf.ac.uk/wbg/pdf/imagene_usermanual.pdf] | No, Uploaded but Not Parsed |
| Nimblegen (Roche) | .NDF | N/A, Contribution Appreciated. | -- | No, Uploaded but Not Parsed |
| ScanArray | --| N/A, Contribution Appreciated. | -- | No, Uploaded but Not Parsed |
| UCSF Spot | .SPT | N/A, Contribution Appreciated. | -- | No, Uploaded but Not Parsed |
| MAGE-TAB | .ADF | Need to create | [More on MAGE-TAB Files|https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Caarray007] | No, Uploaded but Not Parsed |
{tip:title=Good to Know}Before you submit your new array design file for uploading, make sure that you have selected the [correct file format|https://wiki.nci.nih.gov/x/Nxo9Ag#6-CurationTools-ArrayDesignFormatFilesincaArray] from _File Format_ drop down list. The default selection of 'Automatic' from File Format might fail in recognizing some file types.{tip}
h3. Further Readings on Uploading Array Design Files into caArray
# [Importing an Array Design into caArray|https://wiki.nci.nih.gov/x/Nxo9Ag#6-CurationTools-ImportinganArrayDesign]
# [Import Array Designs Use Case Specification|https://gforge.nci.nih.gov/svnroot/caarray2/trunk/docs/requirements/use_cases/manage_array_designs_use_case_specification.doc]
# [Check Existing Array Design Files on caArray|https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Caarray002#Step_1_.28for_all_array_platforms.29:_Check_the_availability_of_Array_Design_File.28s.29.]
# [Managing Array Designs|https://wiki.nci.nih.gov/x/Nxo9Ag#6-CurationTools-ManagingArrayDesigns]
h3. Useful Tools
[Spotter file to ADF Converter|http://www.ebi.ac.uk/cgi-bin/microarray/gal2adf2mart.pl]. This converter tool can convert .GAL design file for Biorobotics, Genetix, Agilent, Clontech, Virtek to MAGE-TAB formatted Array Design File (ADF).
h2. Have a comment?
Please leave your comment in the [caArray End User Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=6&t=577].
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