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Applicable Releases:</strong> caArray 2.2.0 and above

<strong>Date entered:</strong> 03/30/2009

caArray Usage

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question}}Question: Which File Can Be Parsed into caArray? What is The Benefit of File Parsing? {{questionEnd

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<b>Table 1. Files That Can Be Importedinto caArray</b>

File Types

Imported after validation and processing

Imported without validation and parsing

Raw/processed data files

  • Affymetrix CEL, CHP
    GenePix GPR
  • Illumina CSV
  • For GenePix .GPR files, the sample names are already implicit in the data files themselves. If such files are imported as part of a set of files including a MAGE-TAB SDRF, the SDRF file must contain all the sample names that are implicit. Otherwise, a validation error occurs. |
  • Affymetrix DAT, RPT, TXT,and EXP
  • gilent TSV, TXT
  • Illumina IDAT, TXT
  • ImaGene TIF, TXT
  • Nimblegen GFF, TXT
  • ScanArray CSV
  • GEO SOFT
  • GEO GSM |

    Array Design files

  • Affymetrix CDF, PGF CLF
  • Illumina Design CSV
  • Genepix GAL
  • Note: These can be uploaded, validated and imported only through the Manage Array Design feature described in Managing Array |
  • Agilent CSV, XML
  • UCSF Spot SPT
  • ImaGene TPL
  • Nimblegen NDF
  • Note: These can be uploaded, and imported only through the Manage Array Design feature described in Managing Array |

    MAGE-TAB files

  • MAGE-TAB SDRF (Sample and Data Relationship Format)
  • MAGE-TAB IDF (Investigation Description Format) only, no referenced SDRFs
    Note: Only one IDF is allowed per import, since the import is in the context of a single experiment. |
  • MAGE-TAB ADF
  • MAGE-TAB Data Matrix |

Benefit of File Parsing

For the data that are parsed into caArray, an analytical service (like geWorkbench) can pull them 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 interested, instead of having to retrieve the entire data file contents.

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