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  • Changing FDR in DESeq2

    Could anyone please tell me how to change the FDR from default (0.1) to 0.05 in DESeq2.

    Thanks
    Priya

  • #2
    at which step?

    Comment


    • #3
      Thanks Jeremy for replying to my question. I would like to change FDR before/while calculating the differential gene expression. I'm using DESeq2 1.2.10 Vignette. The entire differential expression steps are distilled to one step DESeq(). That is where I'm having problem.

      Priya

      Comment


      • #4
        You can choose whatever adjusted p-value cutoff you like after DESeq() and results(). DESeq() does not perform multiple test correction.

        dds <- DESeq(dds)
        res <- results(dds)
        resSig <- res[which(res$padj < 0.05),]

        The independent filtering in results() has an argument 'alpha', which is used to optimize a cutoff on mean normalized count, to maximize the number of genes with padj < alpha.

        So you can do:

        res <- results(dds, alpha=.05)
        resSig <- res[which(res$padj < 0.05),]

        Lots of useful information in ?DESeq and ?results.

        Comment


        • #5
          Thanks, Michael !! Think I missed it somewhere.

          Priya

          Comment


          • #6
            The object res has the results for all of the genes and their FDR adjusted p-values. I always just merge res with the corrected count data and then write it all out to a tab delimited table then you have all the information that you can put in as a supplementary file.

            Comment


            • #7
              Thank you, Jeremy !!

              Comment

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