Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Galaxy to Cummerbund Data Import Issue

    Hi,

    I am having issues importing my cuffdiff data (generated through Galaxy) into cummerbund. When using R3.1.1 and cummerbund2.7.2 (or 2.6.1) I get the following warning and some processes (like dispersion plot) do not work:

    Warning messages:
    1: attributes are not identical across measure variables; they will be dropped

    When trying to make a dispersion plot in v.2.7.2....
    Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
    replacement has 1 row, data has 0

    This issue is resolved if I use cummerbund 1.2.0, but I would like to use the latest version of cummerbund to take advantage of newer plotting functions, like dispersion plot and PCA.

    Can anyone give me advice as to what this issue is and how it can be resolved?

    Thanks!

  • #2
    I got the same error :
    Warning messages:
    1: attributes are not identical across measure variables; they will be dropped

    Did you get any solution?? please let me know...
    Second thing, I think its not an error, its just warning message so we can just ignore them and go on ....
    anybody has idea ?



    Originally posted by mclo41 View Post
    Hi,

    I am having issues importing my cuffdiff data (generated through Galaxy) into cummerbund. When using R3.1.1 and cummerbund2.7.2 (or 2.6.1) I get the following warning and some processes (like dispersion plot) do not work:

    Warning messages:
    1: attributes are not identical across measure variables; they will be dropped

    When trying to make a dispersion plot in v.2.7.2....
    Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
    replacement has 1 row, data has 0

    This issue is resolved if I use cummerbund 1.2.0, but I would like to use the latest version of cummerbund to take advantage of newer plotting functions, like dispersion plot and PCA.

    Can anyone give me advice as to what this issue is and how it can be resolved?

    Thanks!

    Comment


    • #3
      Hi JP,

      Turns out that warning message is something that can be ignored. The error message is a result of Galaxy output not being entirely compatible with cummeRbund. To resolve this issue, run the cufflinks pipeline via command line.

      Comment


      • #4
        Thank you mclo41
        Yes, I did compete my run using command lines on my server and these were just warnings on cummRbunds, So, I just ignored then because there were not errors....
        Thank you again
        jp


        Originally posted by mclo41 View Post
        Hi JP,

        Turns out that warning message is something that can be ignored. The error message is a result of Galaxy output not being entirely compatible with cummeRbund. To resolve this issue, run the cufflinks pipeline via command line.

        Comment


        • #5
          Hi,

          I ran the cufflinks pipeline by using command line, but still facing the same problem.

          Could some tell me how to solve this issue?

          Thanks

          Originally posted by mclo41 View Post
          Hi JP,

          Turns out that warning message is something that can be ignored. The error message is a result of Galaxy output not being entirely compatible with cummeRbund. To resolve this issue, run the cufflinks pipeline via command line.

          Comment


          • #6
            Please check my answer out on Iplant regards to importing Cuffdiff2 data: http://ask.iplantcollaborative.org/q...-gff3gtf-file/

            I hope this helps a bit.

            -Zapages

            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
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            9 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
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X