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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 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 and Illumina CSV files, see MAGE-TAB SDRF , the SDRF file must contain all the sample names that are implicit. Otherwise, a validation error occursValidation Rules, items 1 and 2.

• Affymetrix DAT, RPT, TXT, and EXP
  
• gilent Agilent TSV, derived TXT
  
• Illumina IDAT, TXT
  
• ImaGene TIF, TXT
  
• Nimblegen GFF, Raw or Derived 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

• , 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 files

• 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.