Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DiffBind: error with dba.count

    Hello,

    I've been using DiffBind to analyze some ATAC-seq peak data. Briefly, peaks in these datasets represent sites of open chromatin. DiffBind seems to do a very good job, but I've encountered an error in my most recent comparison. Here's the R code:

    Code:
    > library(DiffBind)
    > diffpeaks <- dba(sampleSheet = "metadata.csv")
    # suppressed output
    > diffpeaks <- dba.count(diffpeaks)
    # suppressed output
    [B]Error in if (sum(tokeep) < length(tokeep)) { : 
      missing value where TRUE/FALSE needed[/B]
    In addition: Warning message:
    In dba.multicore.init(DBA$config) :
      Parallel execution unavailable: executing serially.
    I've bolded the actual error. I've looked through the dba.count() code, and I can't tell where the error is coming from. My best guess is that it's from the pv.count() function, but I can't seem to find anything about it anywhere. This is really a mystery to me (and I thought I knew what was going on in R too )...

    I’ve selected subsets of the metadata with varying sizes--sometimes it works, and sometimes I get the same error. This leads me to believe that it isn’t a memory issue.

    Does anyone have any ideas about this?

    Thanks for any help,

    Blake

  • #2
    It appears that DiffBind can't handle the "-" character (minus sign/hyphen) in the file names. Remove them and it should work!

    Cheers-
    Rory

    Comment


    • #3
      Hi Blake, just curious if this has been resolved. I'm getting the same exact error with my data; while I've pinpointed the exact subset where the error is coming from, my file names all have alphanumeric characters.

      Comment


      • #4
        Unfortunately, I have not resolved the issue yet. I'm just curious, what kind of machine are you running DiffBind on? I've used it several times without error on a Unix based HPC. But ever since I've tried using it on my windows computer, I get this error. The HPC has been down for maintenance, so I haven't been able to see if running it there solves the problem. I'll post my results whenever the cluster is back up.

        Comment


        • #5
          Thanks for your response. I'm running it on my Windows computer through RStudio. We do have a Unix based HPC, but I've never tried running R there. I'll give it a shot and see how it goes.

          Comment


          • #6
            Update: I ran the same set of data on our Unix based HPC and it worked!

            Comment


            • #7
              That's good to hear. I really don't have any sort of an idea of why DiffBind (specifically dba.count()) does not seem to work on Windows. I look forward to when I can use our HPC again! Thanks for the update.

              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, 03-27-2024, 06:37 PM
              0 responses
              16 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-27-2024, 06:07 PM
              0 responses
              13 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              56 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              70 views
              0 likes
              Last Post seqadmin  
              Working...
              X