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From what I was able to observe, the annotation files (CSV) for NetAffx Hg-U133 Plus 2.0 is updated regularly.

However, from glancing at the CSV files (NA35: 2015 & NA22: 2007), I can't seem to notice any glaring difference between the two.

Does anyone know what information is actually being updated? I assume it may be gene identifiers for different databases, but wanted to make sure.

Thanks.

Below are the files I downloaded and examined from Affymetrix website (you need an account to download archived annotation files)

  • HG-U133_Plus_2 Annotations, CSV format, Release 22 (20 MB, 5/31/07)
  • HG-U133_Plus_2 Annotations, CSV format, Release 35 (33 MB, 4/16/15)
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After checking the files myself, it does seem like gene identifiers indeed have been updated. Some that were missing have been added with identifiers and some have additional identifiers now.

Among some other things that were updated from 2007 include:

  • Genome version NCBI Version 36.1 => GRCh37
  • Alignments
  • Gene title
  • Gene symbol

Thought this would be a good reference for those who may be looking into older researches involving microarrays. I will be sure to check the files more carefully before posting questions like this one.

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  • $\begingroup$ Nice you could answer yourself the question! (you can mark it as solved yourself) But I would still use the most up to date annotation of microarrays when using "old" data. However, I agree that some differences between analysis might be due to using different annotations. $\endgroup$
    – llrs
    Oct 10, 2017 at 7:34

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