Entering edit mode
6 weeks ago
mnx0723
•
0
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?
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.
Thank you. I can get ASHG19AP1B 's gene ID, But still remain (+)E1A_r60_ ID. And additionally discovered new type in this file.
These probe ID also be problem to me
Those are controls. Spike-in etc.