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  • goseq errors

    Hi All
    I am using R 2.14.2 version. I have tried running the goseq tutorial code and it fails to perform the probability weighting function calculation (pwf).
    I am not sure what is going on, here is the part I am stuck at:

    > library("goseq")
    Loading required package: BiasedUrn
    Loading required package: geneLenDataBase
    > library("edgeR")
    Loading required package: limma
    > table.summary=read.table(system.file("extdata","Li_sum.txt",package='goseq'),
    + sep='\t',header=TRUE,stringsAsFactors=FALSE)
    > counts=table.summary[,-1]
    > rownames(counts)=table.summary[,1]
    > grp=factor(rep(c("Control","Treated"),times=c(4,3)))
    > summarized=DGEList(counts,lib.size=colSums(counts),group=grp)
    > disp=estimateCommonDisp(summarized)
    > disp$common.dispersion
    [1] 0.05688364
    > tested=exactTest(disp)
    > topTags(tested)
    Comparison of groups: Treated-Control
    logFC logCPM PValue FDR
    ENSG00000127954 11.557868 6.680782 2.574972e-80 1.274766e-75
    ENSG00000151503 5.398963 8.499425 1.781732e-65 4.410322e-61
    ENSG00000096060 4.897600 9.446635 7.983756e-60 1.317479e-55
    ENSG00000091879 5.737627 6.281841 1.207655e-54 1.494654e-50
    ENSG00000132437 -5.880436 7.951978 2.950042e-52 2.920896e-48
    ENSG00000166451 4.564246 8.458263 7.126763e-52 5.880292e-48
    ENSG00000131016 5.254737 6.607187 1.066807e-51 7.544766e-48
    ENSG00000163492 7.085400 5.126627 2.716461e-45 1.681014e-41
    ENSG00000113594 4.051053 8.602951 9.272066e-44 5.100255e-40
    ENSG00000116285 4.108522 7.864828 6.422468e-43 3.179507e-39
    > genes=as.integer(p.adjust(tested$table$PValue[tested$table$logFC!=0],
    + method="BH")<.05)
    > names(genes)=row.names(tested$table[tested$table$logFC!=0,])
    > table(genes)
    genes
    0 1
    19535 3208
    > pwf=nullp(genes,"hg19","ensGene")
    Loading hg19 length data...
    Error in pcls(G) : initial parameters not feasible

    I will appreciate any help on this matter.
    Rocky

  • #2
    I just ran this on R 2.14.1, windows 7 and it works great. No errors until the last step.

    Comment


    • #3
      Hi
      I met the same error when doing goseq, but it worked well before, I can't figure out what's going on now, have you solved it yet?

      Comment


      • #4
        Weird, 2 days ago I got the same error and I thought I was doing something wrong, I hope it is about the version of R.

        Comment


        • #5
          Hi sazz,
          My R version: "R version 3.1.0 (2014-04-10)". I used Linux and Mac both have the same error. If you figure out the reason, please let me know. Thank you a lot.

          Comment


          • #6
            Hi sazz,
            I don't think it came from wrong code. And I check the record I did before, at May 13th, the same code and input data but had no error. And also the same R version(3.1.0).
            Now the error trace showed:
            5 stop("initial parameters not feasible")
            4 pcls(G)
            3 makespline(bias.data[w], DEgenes[w])
            2 nullp(gene.vector, bias.data = countbias, plot.fit = T)
            Hope this can be a hint for you.

            Comment


            • #7
              I updated my R version (3.1.0) and it works now. Hope this helps..

              Comment


              • #8
                Hi sazz
                Yes. I re-installed my R(the same version as before 3.1.0), and it works now. Thank you very much!

                Comment


                • #9
                  Hi,
                  After I changed to goseq's new version(1.16.2), without re-install R(because it already the latest version), the error gone. So maybe goseq version is also important. Thanks all!

                  Comment

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