Microarray pbrobe ID to gene ID problem

Question

[mnx0723]

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.

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?

Answer 1

[GenoMax]

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.

[mnx0723]

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

[GenoMax]

Those are controls. Spike-in etc.