Select one microarray probe for gene (Affymetrix) - tools 2025?

Question

[Nona]

Good afternoon,

I would like to select one probe per gene (currently after mapping to ENSEMBL IDs several probes map to one gene). I have searched online however I find many old posts about this topic and I wonder if there is maybe a better / up-to-date tool available, which I should use instead? I found for example the option to do it with the R jetset package (basically calculate a score for each probe and take the probe with the highest score).

Thanks for any input!!

[GenoMax]

Why do you want to select just one probe since microarray data analysis software packages will account for all of them during analysis. Since you added the word affymetrix the question is likely about that kind of data? Affymetrix microarray annotations generally have the necessary gene information so no manual mapping to ID's should be required.

Or is this question about creating a probe pair to do PCR?

[Nona]

Thank you for your reply. I am combining RNA-seq and Microarray (mostly Affymetrix) in one cohort, I therefore need to select one probe mapped to one gene in order to combine it with the RNA-seq data.

[GenoMax]

These past threads may be worth taking a look at :

How to merge microarray and RNA-SEQ expression data for DEG analysis?
Integration of RNA-Seq data with microarray data
Combining Microarray and RNAseq data

Since microarrays work on probe intensities (not counts) not sure how you are going to select just one probe as a representative.

[Nona]

Thank you for the links, I will check!