Instructions for preparation and upload of Affymetrix data into mAdb

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Instructions for preparation and upload of
Affymetrix data into mAdb
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Download and install free Affymetrix software
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Affymetrix importing CEL files into GCOS
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NOTE Importing CEL files into GCOS erases them
from their original folder. You may therefore
wish to create a copy of the folder for import.
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Important note for importing CEL files into GCOS

• Successful import requires that the directory
  containing the .CEL files also contain .EXP files
  for each chip. Ordinarily these are generated by
  the software during the chip scan. For situations
  in which .EXP are not available (e.g. .CEL files
  downloaded from a public repository such as GEO),
  GCOS provides a semi-automatic workaround.
• If .EXP files are absent, the import process
  described on the previous slide, while reporting
  errors, automatically extracts .EXP files to the
  same directory. Edit these files as described
  below in step 2.
• Open each .EXP file in a text editor, and
  immediately after Pixel Size, tab, type 1.56 and
  save. Once this is done for all files, repeat the
  import process described on the previous slide.

If the number of chips makes this workaround
impractical, Affymetrix Tech Support
(888-DNA-CHIP) distributes an executable which
when pointed to the .CEL file directory,
generates the completed .EXP files.
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Affymetrix - generating metrics.txt files in GCOS

• Select a .CEL file and right click gt Analyze, to
  generate the .CHP file.
• NOTE Selecting more than one .CEL file (Shift
  key) generates all the respective .CHP files at
  once. The open window will automatically display
  them all when viewed using the Pivot tab (below)
  the multiple files appear as a spreadsheet.

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Affymetrix - generating metrics.txt files in GCOS
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Uploading Affymetrix arrays into mAdb
The metrics and CEL files are now ready for
upload. From the mAdb Gateway page click Upload
Array data, select your project, and open the
following form.

• For the Data File box, Browse to the metrics
  (.txt) file. (Note- Affymetrix software also
  generates .DAT files do not upload them.)
• Browse to the corresponding .CEL file in second
  box.
• Then click on the Continue button to submit the
  files for upload.

Note If you use a custom chip design, contact us
at info_at_ericbrc.org so that we may accurately map
data to features.
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Confirming Affymetrix Upload
Clicking the Continue button opens a confirmation
page. Check that the uploaded data files are
correct. Add names, descriptions or comments, and
associate MIAME protocols to this array on the
bottom half of the form. (Option - protocols may
be attached later via the Edit link on the
projects Summary Report page.) Clicking on the
Confirm button puts the array in queue for
processing by a mAdb administrator.
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Affymetrix Data Upload Summary

• Download and install the Affymetrix GCOS
  software, and install the library files for the
  anticipated experiments.
• In GCOS, import the experiments CEL files,
  generate CHP files, and extract the metrics
  files.
• On the mAdb Gateway page, click Upload Array
  Data, choose Array Type Affymetrix and the
  appropriate project.
• On the Upload page, Browse to the appropriate
• data file (metrics - .txt file)
• CEL file
• On the Confirm page, verify the correct files for
  upload. Enter experiment data (array name,
  description, etc.). Click Confirm.
• From the mAdb Gateway page, click Status of
  Uploads to monitor progress.
• Close browser when finished (for security).