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  • error in cummeRbund dispersionPlot

    Hi,

    I am trying to run cummeRbund with the cuffdiff results.
    these is my workflow:

    Code:
    library(cummeRbund)
    
    setwd("cummeRbund/")
    
    cuff <- readCufflinks(dir=cuffFile_dir, gtfFile="merged.gtf", genome="dm3" , rebuild=TRUE)
    everything seems to run good. all tables are ok, but I am getting these warnings:
    Code:
    Warning messages:
    
    1: attributes are not identical across measure variables; they will be dropped 
    ...
    8: attributes are not identical across measure variables; they will be dropped
    I have read here, that these messages can be ignored, so I am not sure they're connected to my problem.

    I am than trying to execute the DispersionPlot commend. But this gives me an error:

    Code:
    > disp<-dispersionPlot(genes(cuff))
    > disp
    [B]Error in seq.default(min, max, by = by) : 
      'from' cannot be NA, NaN or infinite[/B]

    Does anyone have an idea why I get this error?
    How can I prevent this from happening?

    thanks

    Assa

    #####
    > sessionInfo()
    R version 3.1.1 (2014-07-10)
    Platform: x86_64-apple-darwin13.1.0 (64-bit)

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

    attached base packages:
    [1] grid stats4 parallel stats graphics grDevices utils
    [8] datasets methods base

    other attached packages:
    [1] mgcv_1.8-3 nlme_3.1-118 cummeRbund_2.8.2
    [4] Gviz_1.10.2 rtracklayer_1.26.1 GenomicRanges_1.18.1
    [7] GenomeInfoDb_1.2.2 IRanges_2.0.0 S4Vectors_0.4.0
    [10] fastcluster_1.1.13 reshape2_1.4 ggplot2_1.0.0
    [13] RSQLite_1.0.0 DBI_0.3.1 BiocGenerics_0.12.0

    loaded via a namespace (and not attached):
    [1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2
    [4] BatchJobs_1.5 BBmisc_1.8 Biobase_2.26.0
    [7] BiocParallel_1.0.0 biomaRt_2.22.0 Biostrings_2.34.0
    [10] biovizBase_1.14.0 bitops_1.0-6 brew_1.0-6
    [13] BSgenome_1.34.0 checkmate_1.5.0 cluster_1.15.3
    [16] codetools_0.2-9 colorspace_1.2-4 dichromat_2.0-0
    [19] digest_0.6.4 fail_1.2 foreach_1.4.2
    [22] foreign_0.8-61 Formula_1.1-2 GenomicAlignments_1.2.1
    [25] GenomicFeatures_1.18.2 gtable_0.1.2 Hmisc_3.14-5
    [28] iterators_1.0.7 labeling_0.3 lattice_0.20-29
    [31] latticeExtra_0.6-26 MASS_7.3-35 Matrix_1.1-4
    [34] matrixStats_0.10.3 munsell_0.4.2 nnet_7.3-8
    [37] plyr_1.8.1 proto_0.3-10 R.methodsS3_1.6.1
    [40] RColorBrewer_1.0-5 Rcpp_0.11.3 RCurl_1.95-4.3
    [43] rpart_4.1-8 Rsamtools_1.18.1 scales_0.2.4
    [46] sendmailR_1.2-1 splines_3.1.1 stringr_0.6.2
    [49] survival_2.37-7 tools_3.1.1 VariantAnnotation_1.12.3
    [52] XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0
    Last edited by frymor; 11-10-2014, 05:22 AM.

  • #2
    I'm having the same issue if anyone has a solution?

    Comment


    • #3
      Same issue for me. In other forum I read that "#" character in gtf file have to be removed. In my case I dont have # but still have the error.

      Thanks.
      Last edited by chodar; 03-09-2015, 09:44 AM.

      Comment


      • #4
        I had the same issue as well - it was caused by some extremely low dispersion (and count) values. Some were of the order of 10e-308, which is lower than the minimum floating point value supported by R (on my architecture anyway). I set these to 0 and the plot then worked.

        I need to read up a bit more about cuffdiff - obviously it normalises the count values, but I can't see why any should be much less than 1.

        Greg

        Comment


        • #5
          how to delete most 0 values

          Originally posted by Greg Deakin View Post
          I had the same issue as well - it was caused by some extremely low dispersion (and count) values. Some were of the order of 10e-308, which is lower than the minimum floating point value supported by R (on my architecture anyway). I set these to 0 and the plot then worked.

          I need to read up a bit more about cuffdiff - obviously it normalises the count values, but I can't see why any should be much less than 1.

          Greg
          I have same trouble when I draw disperse graph. Do you know how to code to delete most small values and small counts e.g. 2e-168

          Comment

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