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Contents

Topic: caArray Usage

Release: caArray 2.0 and above

Date entered: 04/20/2009

Question

caArray's File Validation

I was importing MAGE-TAB array data files and related annotation files, but my .srdf file received an error message as "Failed Validation". Why?

Answer

In caArray, many types of files can be uploaded, but not all files can be validated. The validation process is only for the data files associated with experimental samples, such as: array design files, array data files, and array annotation files (caArray014 Which Files Can Be Uploaded into caArray?). The validation process may occur implicitly (array design file) or explicitly (all other array-related annotation or data files).

File validation verifies if the data content adheres to a certain format. It does not evaluate the accuracy of the data from scientific viewpoint. A validation error can be structural or content-based. Validation can fail for one or more of the following reasons:

  • Format unknown (Errors are based on file extension and array type)
  • Reference file not found (e.g. array data file is listed in MAGE-TAB .SDRF, but not uploaded)
  • File incomplete
  • Vocabulary failure (annotation terms has to be in supported ontology and declared in .IDF file)

If a file fails to be validated, this file can not be imported into caArray, unless the:

  1. Error is fixed
  2. Validation process is bypassed by changing file type
  3. Import process is bypassed by uploading the file as a supplemental file

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