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!
1 answer
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.
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