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  • DeSeq and EdgeR Annotation

    Hi all,

    I have a gene list with refseq names as input for DeSeq and EdgeR (using both), I want to add official gene names for the output as well. I tried the following in EdgeR but it did not work:

    library(org.Hs.eg.db)
    idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)
    y <- y[idfound,]
    dim(y)

    Any good ways to do it?

  • #2
    The oral carcinoma case study in the edgeR User's Guide gives a fully worked example in which this is done.

    Make sure you are using a recent version of edgeR.

    For more detailed help about how to use Bioconductor annotation packages, it would be best to post a question to the Bioconductor mailing list.

    Gordon

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