How can I convert mouse probe ID's from GEO (TC0500001894.mm.2) in this format - to a readble gene symbol?

Question

[Nathan]

Hi, I've downloaded an analyzed dataset from GEO (analyzed by the GEO2R online tool), this is the platform that was used: [Clariom_S_Mouse] Affymetrix Clariom S Assay, Mouse (Includes Pico Assay) and this is how the probes ID look like:

TC1500000432.mm.2 TC1300000045.mm.2 TC1000000508.mm.2 TC1300001353.mm.2 TC1400002215.mm.2

How can I convert them (online, or by code) to a readable gene symbol? (or UniProt ID)

I tried to search before I posted, but didn't find any relevant solution. Thanks!

Answer 1

[Trivas]

I would look into the biomaRt package (see https://bioconductor.org/packages/release/bioc/html/biomaRt.html). The vignette goes into a little more detail than I think the average user needs, but it's very simple to follow along and pick which gene names you want out of it. I don't remember if biomaRt can go directly to gene symbol but there are plenty of converters (I use https://www.biotools.fr/mouse/ensembl_symbol_converter) if you can end up at either UCSC, Ensembl, or refSeq IDs.