Affymetrix Human Genome U133B Array - Series Matrix File Annotation problem

Question

[tyasird]

Hello,

I am using NCBI (GSE61335) dataset for gene expression analysis.

I have analysed CEL Files there is no problem. Usually when I need to convert Probset Ids to gene symbol, I use Soft file or affymetrix annottion file which everyone can download in website.

But in this dataset (GSE61335) , I was not able to convert Probset IDs to Gene Symbol because Series matrix files have different Probset IDs.

what is wrong this series matrix file? how can I convert these probset Ids to gene symbol?

series matrix file

annotation file

Answer 1

[Ahill]

Use the platforms (GPL) specified in the GSE series record to map the probeset IDs to entrez gene IDs. From the GSE annotations, this series used two custom platforms defined by "custom" CDFs not generated by Affymetrix. The two platforms are: GPL19180 and GPL19184. Browsing the entry for GPL19180, you can see several of the non-standard probeset IDs in your screenshot, like 1_at. The GPL records include mappings from the probeset IDs to entrez gene IDs (e.g. here for the first platform)

[tyasird]

Thank you for your response.

GPL records includes ID-ENTREZ_GENE_ID-SPOT_ID.. Still I dont access any gene symbols. how can I find it?

edit: I used David Gene Accession Conversion Tool from GPL records GENEID to find GENESYMBOL, is it ok?

[Ahill]

Yes, using DAVID should be fine. A number of annotation databases/tools should be able to convert from Entrez (NCBI) Gene ID to Gene Symbol. One other option would be Uniprot's ID conversion utility: https://www.uniprot.org/uploadlists/.