This page contains deposit recommendations, instructions and templates specific to Affymetrix arrays. These recommendations simply describe what we believe is the easiest batch deposit method for the majority of Affymetrix researchers, but keep in mind that Affymetrix data may be submitted to GEO using any of the deposit options described on the Submitting Data page. If you need additional guidance for your submission, please e-mail us with a brief description of the type of data you are trying to submit, and one of our curators will quickly get back to you.

The GEOarchive spreadsheet-based submission method is recommended for Affymetrix deposits.
With this submission option, you provide the following components:

1. An Excel metadata spreadsheet containing descriptive information and protocols for the overall experiment and individual Samples (see templates below).
2. CEL files
3. Processed data, usually probe set summary data generated by the primary analysis software (e.g., Expression Console, Microarray Suite 5.0, Genotyping Console, GTYPE/CNAT, GTGS, Tiling Array Software, or GeneChip-compatible/other 3rd-party software). These data may be submitted either as CHP files or a matrix table (see examples in templates below). Please submit the data used to draw the conclusions of your study. For instance, do not submit CHP files analyzed with MAS5.0 if your submission is related to a publication based on GC-RMA data. In this case, you should submit the GC-RMA probe set summary data instead of MAS5.0 CHP files.

Finding the Platform
On most versions of the metadata spreadsheet you are asked to specify what chip (Platform) you used. Most commercial Affymetrix Platforms are already represented in GEO, to find the accession number (GPLxxx) use the FIND PLATFORM tool.

Custom arrays and alternative probe groupings
You must provide library files (CDF or CLF/PGF) and gene-level probe set annotations when submitting data for custom arrays, or when alternative (custom) probe groupings are used. The probe sequences are also required for custom arrays (probe_fasta or probe_tab files). The gene-level annotations can be included as additional columns in the matrix table containing the scaled or normalized data, or they can be supplied as an external file (e.g. Affymetrix annotation CSV file).

Affymetrix GEOarchive templates and examples

The following Excel files illustrate the structure of different types of GEOarchive Affymetrix data submissions. Each Excel file consists of several spreadsheets, including a metadata template, and metadata and matrix table examples. Click the tabs at the bottom of the spreadsheet window to switch between spreadsheets. Guidelines for the content of each field is provided on the spreadsheets.

3' or Whole Gene Expression Array - CHP file option

3' or Whole Gene Expression Array - Matrix table option

Exon Array - CHP file option

Exon Array - Matrix table option

Tiling Array

SNP Array

Bundle all components (Excel metadata file, CEL files, CHP files or matrix spreadsheet, plus library/sequence/annotation files for custom applications) together into a .zip, .rar, or .tar archive using a program like WinZip, and transfer to GEO by selecting the 'GEOarchive' option on the Direct Deposit page. Incomplete submissions will result in processing delays.