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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #218345
Title: CEL_INTERROGATOR: A FREE AND OPEN SOURCE PACKAGE FOR AFFYMETRIX CEL FILE PARSING

Author
item Nelson, Rex
item Shoemaker, Randy

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/25/2007
Publication Date: 1/12/2008
Citation: Nelson, R., Shoemaker, R.C. 2008. Cel_interrogator: a free and open source package for affymetrix cel file parsing [abstract]. Plant and Animal Genome Conference. Paper No. P867.

Interpretive Summary:

Technical Abstract: CEL_Interrogator Package is a suite of programs designed to extract the average probe intensity and other information for each probe sequence from an Affymetrix GeneChip CEL file and unite them with their human-readable Affymetrix consensus sequence names. The resulting text file is suitable for direct analysis by text editors or the included CEL_retriever program which will extract the probe intensity and other values for a list of Affymetrix GeneChip consensus sequences. This feature will allow the inspection and analysis of individual probe values for a set of sequences identified as being up or down regulated in a microarray experiment. This may allow the user to observe the effect of potential cross-hybridization of the individual probes to more than one target as is possible in many plant species with a history of whole or partial genome duplication. A schematic diagram of the analysis flow of the package as well as user and package availability information will be presented. The package is written in the Perl programming language and will be suitable for execution on any system with Perl 5.8.1 and a Perl interpreter.