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The Specify annotation sequence format drop-down menu allows you to specify the format of the probe sequences associated with your microarrays. Please consult with the manufacturer of your microarrays to determine the exact specification of their probe annotation files. The options available for sequence annotation include:

• None: Assumes that the sequences in the microarray annotation are the probe sequences printed on the array
• Complement: Assumes that the sequence is for the region being interrogated by the array
• Reverse complement: Assumes that the sequence is the reverse complement of the interrogated sequence. This is particularly useful if you have primer sequences as annotations

The Consolidation of identical probe sequences option is available to take into account probes that have identical sequences within the same array. This is particularly common in microRNA arrays, where identical mature miRNA sequence can exist for multiple organisms.

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References

1. Affymetrix Whitepaper on Microarray normalization using Signal Space Transformation with probe Guanine Cytosine Count Correction. Accessed February 17, 2016 http://media.affymetrix.com/support/technical/whitepapers/sst_gccn_whitepaper.pdf
2. Irrizarry RA, Hobbs B, Collin F et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostat. 2003; 4:249-264.

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