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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Background: Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment.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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Number of probe pairs removed by individual filter sets. Summary of number of probe pairs removed from standard probe sets -- those having 16 probe pairs -- by each of the three filter sets. Presented for each custom CDF are the total number of probe sets that survived the cleansing process. Default CDF = 12,387 standard probe sets, Upton CDF = 12,386 standard probe sets, BaFL CDF = 10,981 standard probe sets, BaFL + Upton = 10,927 standard probe sets.
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Figure 4: Number of probe pairs removed by individual filter sets. Summary of number of probe pairs removed from standard probe sets -- those having 16 probe pairs -- by each of the three filter sets. Presented for each custom CDF are the total number of probe sets that survived the cleansing process. Default CDF = 12,387 standard probe sets, Upton CDF = 12,386 standard probe sets, BaFL CDF = 10,981 standard probe sets, BaFL + Upton = 10,927 standard probe sets.

Mentions: Table 1 shows how the custom CDFs were changed relative to the original and Figure 4 compares the frequency with which the indicated number of probe pairs are removed from probe sets for each of the three custom CDFs (e.g. the number of probe sets with zero probe pairs removed, one probe pair removed, two probe pairs removed, etc.)


ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.

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

Number of probe pairs removed by individual filter sets. Summary of number of probe pairs removed from standard probe sets -- those having 16 probe pairs -- by each of the three filter sets. Presented for each custom CDF are the total number of probe sets that survived the cleansing process. Default CDF = 12,387 standard probe sets, Upton CDF = 12,386 standard probe sets, BaFL CDF = 10,981 standard probe sets, BaFL + Upton = 10,927 standard probe sets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Number of probe pairs removed by individual filter sets. Summary of number of probe pairs removed from standard probe sets -- those having 16 probe pairs -- by each of the three filter sets. Presented for each custom CDF are the total number of probe sets that survived the cleansing process. Default CDF = 12,387 standard probe sets, Upton CDF = 12,386 standard probe sets, BaFL CDF = 10,981 standard probe sets, BaFL + Upton = 10,927 standard probe sets.
Mentions: Table 1 shows how the custom CDFs were changed relative to the original and Figure 4 compares the frequency with which the indicated number of probe pairs are removed from probe sets for each of the three custom CDFs (e.g. the number of probe sets with zero probe pairs removed, one probe pair removed, two probe pairs removed, etc.)

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