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  • DESeq and edgeR

    Hi,
    i am using both programs to analyse differential expression.
    i used this manual http://manuals.bioinformatics.ucr.edu/home/ht-seq
    so may script is that:

    library("DESeq");
    conditions <- c("1","2")
    cds <- newCountDataSet(x,conditions)
    cds <- estimateSizeFactors(cds)
    cds <- estimateDispersions(cds,method="blind",sharingMode="maximum",fitType="local")
    res <- nbinomTest(cds,condA="1",condB="2")
    res[order(res$padj), ][1:4,]

    sigDESeq <- res[res$padj <= 0.05, ]
    sigDESeq <- na.omit(sigDESeq)
    sigDESeq <- as.character(sigDESeq[,1])

    library("edgeR");
    group <- factor(c(1,2))
    cdsR <- DGEList(counts=x, group=group)
    cdsR <- estimateCommonDisp(cdsR)
    cdsR <- estimateTagwiseDisp(cdsR)
    et <- exactTest(cdsR, pair=c("1", "2"))

    all <- as.data.frame(topTags(et, n=100000))
    sigedgeR <- all[all$adj.P.Val <= 0.05, ]
    sigedgeR <- na.omit(sigedgeR)
    sigedgeR <- row.names(sigedgeR)

    source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/overLapper.R")
    OLlist <- overLapper(setlist=list(DESeq=sigDESeq, edgeR=sigedgeR), sep="_", type="vennsets")
    counts <- sapply(OLlist$Venn_List, length)
    vennPlot(counts=counts)
    counts

    oveLapp <- OLlist$Venn_List

    $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

    i want to check Differential expression between biological replicates.(here: i have only 2)
    1 & 2 are biological replicates.

    the problem is:
    in edgeR i get 377 significant genes where in DESeq i got 0 (ZERO)

    it looks weird to me, but i do'nt know what i did wrong..

    Any advice!?!?

    Thanks,
    Pap

  • #2
    For the record, Pap cross-posted this question also to another list, where it has been addressed in the thread starting at https://stat.ethz.ch/pipermail/bioco...ch/044178.html
    Wolfgang Huber
    EMBL

    Comment


    • #3
      Hi Wolfgang Huber,
      Thank you!
      i didn't see that someone answer me there

      Comment


      • #4
        I had the similar issue. I used the sharingMode="fit-only", but still Deseq gave me 0 differential genes, whereas edgeR gave over 1000

        I couldn't post to BioC mailist since it was in archive and I just subscribed. So I posted here.

        Comment

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