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  • refseq to entrez for use in GOstats.

    Hi all,

    A question regarding annotations for running GOstats in R.

    I have to gene-lists containing refseq-names which I will use as "universe" and "genes" for the GOstats analysis. However GOstats only take entrez. How do I convert the refseq to entrez? I have tried mappedkeys() but didnt really get to understand it.

  • #2
    Are you having trouble finding the gene to entrez geneid lookup?

    Or you don't know how to do the lookup?

    The gene name to entrez geneid is data is at ...
    ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz

    Comment


    • #3
      Thanks,
      I ran it but got the following error:

      syntax error at refseq2entrez.pl line 26, near ")
      #9 1246500 PROVISIONAL - - NP_047184.1 10954455 NC_001911.1 10954454 348 1190 - -

      my "
      Global symbol "%gene2refseq" requires explicit package name at refseq2entrez.pl line 26.
      Global symbol "%gene2refseq" requires explicit package name at refseq2entrez.pl line 36.
      Global symbol "%gene2refseq" requires explicit package name at refseq2entrez.pl line 37.
      Global symbol "%gene2refseq" requires explicit package name at refseq2entrez.pl line 43.
      Global symbol "%gene2refseq" requires explicit package name at refseq2entrez.pl line 49.
      Global symbol "%gene2refseq" requires explicit package name at refseq2entrez.pl line 50.
      Execution of refseq2entrez.pl aborted due to compilation errors.





      Originally posted by Richard Finney View Post
      Are you having trouble finding the gene to entrez geneid lookup?

      Or you don't know how to do the lookup?

      The gene name to entrez geneid is data is at ...
      ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz

      Comment


      • #4
        it would help if you post your usage of the script and also just a thought is the conversion file in the same directory as you/perl script ?

        Comment

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