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  • How do GO enrichment by GO-id?

    Hi all,

    Now I'm doing some analysis on Green algae which is not common species and exisiting software for GO is not applicable, so I wonder if it can be done by hypergeometric distribution in R?

    I've got GO id for most of the 'genes'(not official gene names) and I found some 'genes' have more than one GO id, how do I edit my data file in this situation?And next, how to do hypergeometric distribution?

    Can anyone help?

    Thanks

  • #2
    Hello xunong

    Hypergeometric distribution is used in case of microarray data.
    Are you using RNAseq data? If yes- then i would suggest to use GOseq R package. You can create your own GO instance and then use it. Also use Wallenius approximation for RNA-seq data.

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    • #3
      Originally posted by reema View Post
      Hello xunong

      Hypergeometric distribution is used in case of microarray data.
      Are you using RNAseq data? If yes- then i would suggest to use GOseq R package. You can create your own GO instance and then use it. Also use Wallenius approximation for RNA-seq data.
      thank u reema,
      yes, it is RNA-seq data, can't wait to try GOseq

      Comment

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