Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Degseq Question

    Hello All,

    I am new here in this awesome forum, new to the topics you guys talking about as well. I've read about Degseq and I'm trying to work on it. So, I have installed the R and Degseq and now as a beginner I am working on the example provided in their manual with sample data that comes with Degseq. they started the example with the following command, which went fine:
    > library(DEGseq)
    Then this:
    >geneExpFile <- system.file("extdata", "GeneExpExample5000.txt",+ package = "DEGseq")

    This one keeps returns this error msg:

    Error: unexpected '=' in "geneExpFile <- system.file("extdata", "GeneExpExample5000.txt",+ package ="


    Any Help is appreciated

  • #2
    Originally posted by Amative View Post
    Then this:
    >geneExpFile <- system.file("extdata", "GeneExpExample5000.txt",+ package = "DEGseq")
    Hey there,

    I had a similar problem when I started with R and DEGseq.
    There is a problem where the R syntax and the DEGseq tutorial collide.

    So in R on the console every line begins with a ">" However you never input this character, it's just there. If you then type a multilin statement, R shows by a "+" that this line is just continuing the line above.

    Therefore if you copy and paste the examples, you have to remove the > and + characters, as in:
    geneExpFile <- system.file("extdata", "GeneExpExample5000.txt", package = "DEGseq")

    Also "r getting started" is a good google query to get started with R.

    Best,
    Simon

    Comment


    • #3
      Thanks Simon,

      geneExpFile <- system.file("extdata", "GeneExpExample5000.txt",+ package = "DEGseq")

      should be

      geneExpFile <- system.file("extdata", "GeneExpExample5000.txt", package = "DEGseq")

      SO, I just removed the + sign )

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X