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At the heart of Affymetrix
Informatics is the data generated from a microarray. Affymetrix provides
a variety of open solutions to gain access to these data from file
format documentation to open source code.
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Data from Affymetrix is only as powerful as one's ability to intersect
them with the genomic information represented on the array. Affymetrix
NetAffx site offers a web-based
user-interface to retrieve these annotation information. These same
annotation information can be incorporated within a software application
through the use of the NetAffx SDK.
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View a table of all available resources hosted
through the NetAffx SDK for the analysis of exon expression array. |
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The NetAffx SDK is a set of Application Programming Interfaces (APIs) used to download the annotations available on the Affymetrix NetAffx web site. The NetAffx SDK can also be used to automate the download of library files within an application. |
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This WebTalk presents
an overview of the NetAffx Software Developers Kit and how it can
be used to automate the retrieval of NetAffx annotation files. |
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This forum is intended to be a conduit through which the Affymetrix
Developer's Network supports itself on issues regarding the use
of the NetAffx SDK. |
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Review
this manual to learn how to link directly to NetAffx™ probe
set summaries from within your own applications or web sites using
a convenient deep link URL. |
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Analysis of Affymetrix
microarrays often is focused on comparing samples that have different
attributes. Affymetrix core software like GCOS and Command Console
allow users to input sample attributes into the system and associate
these attributes with the array data through simple XML files. The
associated DTD files will aid software developers in gaining access
to this information and maintaining it with its associated microarray
data.
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Sample
attributes in Command Console are stored in *.ARR files. This is the DTD for the ARR files. |
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Sample attributes
entered into the GCOS Process Database can be easily extracted using
Data Transfer Tool into XML files. This is the DTD for the XML files created. |
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This forum is dedicated to the
purpose of discussing reading and writing sample attribute data. |
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Following the scanning
of an array, a DAT file is created. Then a grid is applied onto this
file creating a CEL file. The following collection of tools focuses
on the data summarization process to generate the downstream CHP file
that is created after the CEL file is generated.
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The
Affymetrix Power Tools (APT) contains C++ source code for analyzing
Affymetrix data and a set of command line tools. APT contains
several key algorithms of interest around the Affymetrix platform
including: BRLMM, PLIER, RMA, MASv5, DABG, and IterPLIER. APT also
provides key guidance on workflows with pre- and post-processing
steps included as well as code to output the data into Affymetrix
binary CHP files. |
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The MAS5 Stat SDK provides source code for the implementation
of the MAS5 Expression Statistical Algorithm. |
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The Tiling SDK is a set of Application Programming Interfaces
(APIs) used for the analysis of GeneChip tiling arrays. |
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Browse a collection
of information from the Affymetrix Developers' Network.
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The Affymetrix Developers'
Network offers a collection of Affymetrix built software applications
enabling a software developer to replicate the same environment that
Affymetrix customers have for the purposes of software development,
testing, and validation.
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Affymetrix GeneChip
Operating Software (GCOS) is the core instrument control and primary
data generating software for the Affymetrix platform. The Affymetrix
Developers' Network provides a collection of tools and utilities to
ease programmatic integration into GCOS.
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The Affymetrix®
Analysis Data Model (AADM) is the relational database schema the
Affymetrix GCOS, LIMS and MicroDB™ systems use to store GeneChip®
expression results. The prefered mechanism for extracting Affymetrix
results is via direct access to the native Affymetrix data files
(CEL, CHP, CDF). Support for AADM can be obtained through the
AADM
message board. |
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The GCOS Software Developer Kit (GCOS SDK) is a suite
of online material for Affymetrix GCOS client or server customers
and third-party vendors who are looking to develop, customize, and
integrate software applications and systems with the Affymetrix
GCOS system. Support for the GCOS SDK can be obtained through the
GCOS SDK Message Board. |
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Data Transfer Tool allows programmatic transfers
of data between separate GCOS instances. A copy of DTT is automatically
installed with any installation of GCOS. |
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Affymetrix grants its
partners and customers complimentary access to its full collection
of SDK components, documentation, and NetAffx data for evaluation
purposes, internal use, or for redistribution in freeware software
applications through either a variety of OSI-approved opens source
licenses or the GeneChip
Non-Commercial SDK license. Please consult the click-through licenses
associated with each utility for specific licensing information. A
Commercial
SDK Use license is also available (part
number 690050). Please contact devnet@affymetrix.com for more information on obtaining a commercial license, as well as an override
to the open source licenses. |
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Please learn to how SDK modifications to commercial Affymetrix
software can affect support limitations. Details here. |
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