Question: ID mapping: from Rat codelink to Entrez
gravatar for fr
20 months ago by
fr100 wrote:

I am using data from GEO GSE8858. From what I understand, the probes have legacy identifiers (e.g. AA799313_PROBE1, AA799329_PROBE1 etc). I would like to convert these to Entrez or Ensembl ids. Under each platform, I can retrieve the Gene bank accession number using the field "GB_ACC", and use them to map to Entrez ID using mygene.

However, from the 10400 probes, I can only map 3800. Is there a better way to do this?

Thanks in advance

chip-seq • 563 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by fr100

If you click on the platforms link you should be able to get a table of annotations. e.g. GPL5424, GPL5425 and GPL5426.

ADD REPLYlink written 20 months ago by genomax69k

Yes, that is how I am doing it: from the annotations in those, I get the GB_ACC, which I then use to convert to Entrez. But this retrieves a very low number of Entrez ids. (I will edit my question to clarify this)

ADD REPLYlink written 20 months ago by fr100
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