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Microarray pbrobe ID to gene ID problem

I am facing an issue with GSEA while converting dataset from probes to symbols. All files except one have been processed successfully. The problematic file is based on platform GPL26963 (Agilent-085982 Arraystar human lncRNA V5 microarray). I attempted GSEA with all Agilent human chip data.

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This particular file contains three types of probe IDs. Symbol extraction was successful with one type of probe ID:

  • A_23_*

, but I am unable to extract symbols from the following types of probe IDs:

  • (+)E1A_r60_*
  • ASHG19AP1B*

How can I retrieve gene IDs and should I consider using a different program?

microarray
• 1,155 views • link
updated by GenoMax GenoMax • written by mnx0723 • mnx0723

1 answer

Table show here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL26963 has the full annotation table. Some of those ID's are identifiers from a FANTOM CAGE study.

• 0 views • link
written by GenoMax GenoMax

Thank you. I can get ASHG19AP1B 's gene ID, But still remain (+)E1A_r60_ ID. And additionally discovered new type in this file.

  • ASSPINKEIN*
  • CUST*
  • DCP*
  • ERCC*
  • ETG10_*
  • Negative*

These probe ID also be problem to me

• 0 views • link
written by mnx0723 • mnx0723

Those are controls. Spike-in etc.

• 0 views • link
written by GenoMax GenoMax

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