Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GoSeq -unable to calculate pwf!

    hello All!
    I am desperately trying to run this GO analysis on my RNAseq data(human samples).
    I got stuck in creating a pwf file: I have -I guess- successfully created a DE matrix, with ENS id and 0/1 as identifier of diff-non diff expressed genes.
    here is the error message I encounter
    genes
    0 1
    19004 6715
    > pwf <- nullp(genes, "hg19", "ensGene")
    Loading hg19 length data...
    Error in qr.R(qrx) :
    could not find symbol "..." in environment of the generic function
    I noticed that the ENS ids in my matrix are not into double quotes...I am not sure if it really has an effect...I have just followed the manual step by step, but I am not able to figure out why is not going through (and I am newbie in all this).
    Anybody can help?!!

    Manu
    > sessionInfo()
    R version 2.15.2 (2012-10-26)
    Platform: x86_64-apple-darwin9.8.0/x86_64 (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] stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] goseq_1.10.0 geneLenDataBase_0.99.10 BiasedUrn_1.05 edgeR_3.0.8 limma_3.14.4 BiocInstaller_1.8.3

    loaded via a namespace (and not attached):
    [1] AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0 biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-4.2 BSgenome_1.26.1
    [8] DBI_0.2-5 GenomicFeatures_1.10.2 GenomicRanges_1.10.7 grid_2.15.2 IRanges_1.16.6 lattice_0.20-15 Matrix_1.0-12
    [15] mgcv_1.7-22 nlme_3.1-108 parallel_2.15.2 RCurl_1.95-4.1 Rsamtools_1.10.2 RSQLite_0.11.2 rtracklayer_1.18.2
    [22] stats4_2.15.2 tools_2.15.2 XML_3.96-1.1 zlibbioc_1.4.0

  • #2
    Hi,

    The description is a little vague but I think I can help troubleshoot the problem.

    1. Are you sure you are working with 'ensGene' symbols? Could your genes be better classified as something else?

    2. Did you manipulate your ensGene ID's at all? Are you supplying two different types of ids in your complete genes list and DE genes list?

    3. Make sure you are running the correct R version 3.0 and bioconductor version 2.12. I was having issues with older versions and this helped.

    Michael
    Last edited by Michael_RNAseq; 05-30-2013, 09:29 AM.

    Comment


    • #3
      Hi Michael!!!

      Thanks for the hints... Actually I have already updated my R version and now everything works beautifully!!!

      So if it can be helpful for anyone else...!

      Thanks guys!
      Manu

      Comment

      Latest Articles

      Collapse

      • seqadmin
        The Impact of AI in Genomic Medicine
        by seqadmin



        Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
        02-26-2024, 02:07 PM
      • seqadmin
        Multiomics Techniques Advancing Disease Research
        by seqadmin


        New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

        A major leap in the field has
        ...
        02-08-2024, 06:33 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 02-28-2024, 06:12 AM
      0 responses
      21 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-23-2024, 04:11 PM
      0 responses
      69 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-21-2024, 08:52 AM
      0 responses
      77 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-20-2024, 08:57 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X