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  • DEXSeq error:Failed to set up model frames for genes

    Here is how I produced the error:
    annotationfile=file.path(inDir,"Homo_sapiens.GRCh37.68.DEXSeq.chr.gff")
    esc=read.HTSeqCounts(countfiles=file.path(inDir,paste(rownames(samples),"txt",sep=".")),design=samples,flattenedfile=annotationfile)
    sampleNames(esc)=rownames(samples)
    esc<- estimateSizeFactors(esc)
    design(esc)
    condition libType
    H0-R1exoncount H0 paired-end
    H0-R2exoncount H0 paired-end
    H0-R3exoncount H0 paired-end
    H24-R1exoncount H24 paired-end
    H24-R2exoncount H24 paired-end
    H24-R3exoncount H24 paired-end

    esc<- estimateDispersions(esc)

    Everything is working fine until the estimateDispersions step, I got the following warning messages:
    1: In .local(object, ...) :
    Exons with less than 11 counts will be discarded. For more details read the documentation, parameter minCount
    2: In .local(object, ...) :
    Genes with more than 70 testable exons will be kicked out of the analysis. For more details read the documentation, parameter maxExon
    3: In .local(object, ...) :
    Failed to set up model frames for genes ENSG00000000003, ENSG00000000419, ENSG00000000457, ENSG00000000460, ENSG00000001036, ENSG00000001084+ENSG00000231683, ENSG00000001167, ENSG00000001460, ENSG00000001461, ENSG00000001497, ENSG00000001617, ENSG00000001629, ENSG00000001630+ENSG00000240720, ENSG00000001631+ENSG00000243107, ENSG00000002079, ENSG00000002330, ENSG00000002549, ENSG00000002586, ENSG00000002587, ENSG00000002822, ENSG00000002834, ENSG00000002919, ENSG00000003056, ENSG00000003249, ENSG00000003393, ENSG00000003400, ENSG00000003402, ENSG00000003436, ENSG00000003509, ENSG00000003987, ENSG00000004059+ENSG00000106328, ENSG00000004399, ENSG00000004455, ENSG00000004478, ENSG00000004487, ENSG00000004660, ENSG00000004700, ENSG00000004766, ENSG00000004777, ENSG00000004779, ENSG00000004838, ENSG00000004864, ENSG00000004897, ENSG00000004961, ENSG00000004975, ENSG00000005001, ENSG00000005007, ENSG00000005020, ENSG00000005022, ENSG00000005059, ENSG00000005073, ENSG00000005075, ENSG0000000 [... truncated]

    Does anyone know what is the problem?


    sessionInfo()
    R version 2.15.1 (2012-06-22)
    Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

    locale:
    [1] C/en_US.UTF-8/C/C/C/C

    attached base packages:
    [1] stats graphics grDevices utils datasets methods
    [7] base

    other attached packages:
    [1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0

  • #2
    I had the same error and it was fixed by upgrading to the most recent version of DEXSeq (1.2.1 I think).

    Comment


    • #3
      Originally posted by dpryan View Post
      I had the same error and it was fixed by upgrading to the most recent version of DEXSeq (1.2.1 I think).
      Thanks, I will try it.

      Comment


      • #4
        Originally posted by dpryan View Post
        I had the same error and it was fixed by upgrading to the most recent version of DEXSeq (1.2.1 I think).
        I updated DEXSeq to 1.2.1, but it still gives exactly same warning message.

        > sessionInfo()
        R version 2.15.1 (2012-06-22)
        Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

        locale:
        [1] C/en_US.UTF-8/C/C/C/C

        attached base packages:
        [1] stats graphics grDevices utils datasets methods
        [7] base

        other attached packages:
        [1] DEXSeq_1.2.1 Biobase_2.16.0 BiocGenerics_0.2.0

        loaded via a namespace (and not attached):
        [1] AnnotationDbi_1.18.1 DBI_0.2-5 DESeq_1.8.3
        [4] IRanges_1.14.4 RColorBrewer_1.0-5 RCurl_1.91-1
        [7] RSQLite_0.11.1 XML_3.9-4 annotate_1.34.1
        [10] biomaRt_2.12.0 genefilter_1.38.0 geneplotter_1.34.0
        [13] grid_2.15.1 hwriter_1.3 plyr_1.7.1
        [16] splines_2.15.1 statmod_1.4.15 stats4_2.15.1
        [19] stringr_0.6.1 survival_2.36-14 tools_2.15.1
        [22] xtable_1.7-0

        Comment


        • #5
          Originally posted by zhuya5607 View Post
          I updated DEXSeq to 1.2.1, but it still gives exactly same warning message.
          Hmm, in that case I don't know. I was able to track down the error by going through the code for estimateDispersions (I think), which threw an error when trying to call glmnb.fit or something like that. I think the version I had was incorrectly calling the function or something like that. You might give something like that a try or just shoot an email to one of the package maintainers.

          Comment


          • #6
            Hi zhuya5607,

            As dpryan pointed out, I have corrected this in DEXSeq 1.2.1. It is strange that it is giving you troubles also this last version and actually I can not reproduce this error! Would you mind sending me your ExonCountSet object with a reproducible code? so I could take a closer look?

            Alejandro

            Comment


            • #7
              Originally posted by areyes View Post
              Hi zhuya5607,

              As dpryan pointed out, I have corrected this in DEXSeq 1.2.1. It is strange that it is giving you troubles also this last version and actually I can not reproduce this error! Would you mind sending me your ExonCountSet object with a reproducible code? so I could take a closer look?

              Alejandro
              Hi, Alejandro

              I found out why I still got the same error when I updated to DEXSeq 1.2.1. Because I was using R-studio, a Graphical interface tool, which saves the workplace when I log out. So, when I log in to R again after update, it actually loaded the saved workplace in which the old version DEXSeq 1.20 is attached.
              But the weird thing is that the sessionInfo() shows I was using the new version.

              There is no error now when I reload the new version.

              Thanks for your and dpryan's kind help!

              Comment

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