Question: ID mapping: from Rat codelink to Entrez
0
gravatar for fr
20 months ago by
fr100
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1491 users visited in the last hour