Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

              Latest Articles

              Collapse

              • seqadmin
                Genetic Variation in Immunogenetics and Antibody Diversity
                by seqadmin



                The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
                Yesterday, 07:24 PM
              • seqadmin
                Choosing Between NGS and qPCR
                by seqadmin



                Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
                10-18-2024, 07:11 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 11-01-2024, 06:09 AM
              0 responses
              25 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-30-2024, 05:31 AM
              0 responses
              21 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-24-2024, 06:58 AM
              0 responses
              25 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-23-2024, 08:43 AM
              0 responses
              56 views
              0 likes
              Last Post seqadmin  
              Working...
              X