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ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.

Overall CC, Carr DA, Tabari ES, Thompson KJ, Weller JW - BMC Bioinformatics (2011)

Bottom Line: However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms.ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements.Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Bioinformatics and Genomics, University of North Carolina - Charlotte, Charlotte, NC 28223-0001, USA.

ABSTRACT

Background: Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications.

Results: ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms.

Conclusions: ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.

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Workflow: creating the custom CDFs. Workflow for creating the custom BaFL, Upton and BaFL + Upton custom CDFs. The boxes in blue are common steps while the boxes in orange are steps unique to a particular filter set.
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Figure 3: Workflow: creating the custom CDFs. Workflow for creating the custom BaFL, Upton and BaFL + Upton custom CDFs. The boxes in blue are common steps while the boxes in orange are steps unique to a particular filter set.

Mentions: We created three custom CDFs using ArrayInitiative: a BaFL-only custom CDF, an Upton-only custom CDF and a BaFL plus Upton joint CDF. Each filter set required a unique approach for generating the probe set definitions due to the different ways that they were communicated; however, after we defined the probe sets for each filter set, the steps for creating the custom CDFs were identical. Figure 3 shows a graphical summary of the CDF creation workflow.


ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.

Overall CC, Carr DA, Tabari ES, Thompson KJ, Weller JW - BMC Bioinformatics (2011)

Workflow: creating the custom CDFs. Workflow for creating the custom BaFL, Upton and BaFL + Upton custom CDFs. The boxes in blue are common steps while the boxes in orange are steps unique to a particular filter set.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113937&req=5

Figure 3: Workflow: creating the custom CDFs. Workflow for creating the custom BaFL, Upton and BaFL + Upton custom CDFs. The boxes in blue are common steps while the boxes in orange are steps unique to a particular filter set.
Mentions: We created three custom CDFs using ArrayInitiative: a BaFL-only custom CDF, an Upton-only custom CDF and a BaFL plus Upton joint CDF. Each filter set required a unique approach for generating the probe set definitions due to the different ways that they were communicated; however, after we defined the probe sets for each filter set, the steps for creating the custom CDFs were identical. Figure 3 shows a graphical summary of the CDF creation workflow.

Bottom Line: However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms.ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements.Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Bioinformatics and Genomics, University of North Carolina - Charlotte, Charlotte, NC 28223-0001, USA.

ABSTRACT

Background: Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications.

Results: ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms.

Conclusions: ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.

Show MeSH