Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Troubles installing ballgown

    Hi all,
    I have lots of BAM files and I want to use ballgown for differential ewxpression.
    I'm using the manuals (https://github.com/alyssafrazee/ballgown , http://master.bioconductor.org/packa...n/ballgown.pdf)
    in order to install it and use it..
    I have R version 3.1.2 and bioConductor version 3.0. The installation (from the README) seems fine, the last lines are:
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (ballgown)

    The downloaded source packages are in
    ‘/tmp/RtmpNRWjaS/downloaded_packages’

    BUT, when I try to use ballgown() (just to see if it works), I get an error:
    Error: could not find function "ballgown"
    I tried also stattest() and it gave me the same error..
    I tried to use lines from the README and the manual but I got the same error.

    I believe I'm doing something wrong.. can someone help me understand what's going on?
    Thank you!!
    Batel

  • #2
    Did you load ballgown package before trying other commands?

    > library(ballgown)

    Ballgown installed using following commands:

    > source("http://bioconductor.org/biocLite.R")
    > biocLite("ballgown")

    Comment


    • #3
      oh I'm ashamed. I had another troubles installing it earlier so "library" didn't help me than, and somehow I forgot use it after the installation worked..
      Thank you very much!!!

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      25 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      22 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      52 views
      0 likes
      Last Post seqadmin  
      Working...
      X