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Question: How do I import an Affy .TXT file into caArray?

Topic: caArray Usage

Release: caArray 2.0 and above

Date entered: 04/15/2010

Details about the Question

I created a new experiment and put all the .cel, .txt, idf and .sdrf files (all from Affymetrix platform) in one zip folder and tried to upload it. I got an error message saying that the "File type " for the .txt files is Unknown.

Answer

caArray cannot automatically detect the Affymetrix .txt file format during file validation and import. In order for caArray to validate and import the files, users need to manually identify these files to be Affymetrix .txt files.

Steps below outline the procedure necessary to import Affymetrix .txt files into caArray:

  1. Upload all the files (idf, sdrf, .cel, and .txt) in the MAGE-TAB format into caArray
  2. Under "Manage Data" Tab, select all the files with extension of ".txt" files
  3. Click "Change File Type" button for each file
  4. Select "Affymetrix TXT" file type as the new file type
  5. Click on "Save" button
  6. Proceed to valid all the files under "Manage Data" Tab
  7. Upon successful validation, proceed to import all the files

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