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Question: Which file can be parsed into caArray? What is the benefit of file parsing?

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File Types

Imported after validation and parsing

Imported without validation and parsing

Raw/processed data files;
provide numerical values of array data

  • Affymetrix CEL, CHP, CNCHP
  • GenePix GPR*
  • Illumina CSV, Sample Probe Profile TXT, Genotyping processed data matrix TXT, Raw TXT
  • Agilent Raw TXT
  • Nimblegen Normalized Pair Report TXT

    *For more information about GenePix GPR and Illumina CSV files, see MAGE-TAB SDRF Validation Rules, items 1 and 2.
  • Affymetrix DAT, RPT, TXT, and EXP
  • Agilent TSV, derived TXT
  • Illumina IDAT, TXT
  • ImaGene TIF, TXT
  • Nimblegen GFF, Raw or Derived TXT
  • ScanArray CSV
  • GEO SOFT, GSM
    Note: caArray may have new parsers available for data files in the system that are already imported but not parsed. To learn about retrofitting those files, see #Retrofitting Data Files.

Array Design files;
provide the design of an array.

For information about array design file types, see the table in Managing Array Designs.

 

MAGE-TAB files;
used to annotate experiments automatically

  • MAGE-TAB SDRF (Sample and Data Relationship Format)
  • MAGE-TAB IDF (Investigation Description Format) only, no referenced SDRFs
  • MAGE-TAB Copy Number Data Matrix
    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 (not copy number)

Supplemental Files

These cannot be validated nor imported. Files of unknown file type or simply reference files fall under this category. For more information, see #Supplemental Files.

 

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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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Please leave your comment in the caArray End User Forum.

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