Question: Convert illumina id to official gene symbol
0
gravatar for donnieDarko
9 months ago by
India
donnieDarko0 wrote:

I have a list of illumina gene id's that I want to perform some operation, in order to do that i need to convert the illumina id's to their official gene symbols, I have tried the following :

  1. using the platform information from GEO ->failed, contain some gene name as unigene id.
  2. tried to separate out those unigene id's and map them to official symbol-> failed because most of them do not have a official name as per org.hs.eg.db and some of them have more than one name.
  3. I am using RStudio , I cannot choose which gene symbol to choose and how ? I have use AnnotationDbi::select() funcion followed by split() to get individual id's, but I am stuck here :

    k[["Hs.112482"]]

         UNIGENE  SYMBOL                                        GENENAME
    87 Hs.112482 NAALAD2  N-acetylated alpha-linked acidic dipeptidase 2
    88 Hs.112482 CHORDC1 cysteine and histidine rich domain containing 1`
    
  4. also I tried using illuminaHumanv4.db, that too failed for not having all gene information, please help how to proceed from the above step.

ADD COMMENTlink written 9 months ago by donnieDarko0

Those are ID's from NCBI's UniGene database that has since been retired. You can find more information and ways to search in this blog post from NCBI.

You can use Entrez search at NCBI to map these still.

ADD REPLYlink written 9 months ago by GenoMax96k
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