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caArray has the ability to upload the array design file or experiment data from many array providers, even if it doesn't have a parser available yet. Those files will be imported into caArray without being validated or parsed. Even if a file is not parsed, the user will still be able to download the file (through the user interface as well as through the programmatic API), and will be able to associate the file to samples, extracts, and hybridizations. This feature allows data to be shared and help the system identify which new parsers are need developed in the future. For more information on how files are processed by caArray, review caArray017 caArray 017 - What is the meaning of the caArray Status of Importing - Imported versus Imported Not Parsed?.

The following table from the caArray User Guide (page 78) summarizes the file types that caArray currently supports with full validation and parsing as well as those that can be imported without validation and parsing. Array data-related file types can also be found on the caArray user interface: Data -> Manage Data - Change File Type.

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For the data that are parsed into caArray, an analytical service (like geWorkbench) can pull the data out using the programmatic API and perform analysis on it or plot graphs from it etc. Another example is web Genome, a caArray client, which pulls parsed data from caArray experiments and plots log ratio values against the chromosome location. With parsed data, a client can ask for quantitative types (columns) of data of interest, instead of having to retrieve the entire contents of the data file.

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