Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • [solved]cummeRbund error message

    Running cummeRbund gives me the following error:

    > cuff_data <- readCufflinks("~/cufflinks/control")
    > csDensity(genes(cuff_data))
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (error in statement: near ")": syntax error)


    Anyone know why? It workes with a different sample.
    Last edited by Palgrave; 10-17-2013, 12:42 PM.

  • #2
    Solved by removing cuffData.db from directory.

    Comment


    • #3
      Dear all,
      any suggestion about this issue I have?

      I run the following commands:
      > library (cummeRbund)
      Loading required package: RSQLite
      Loading required package: DBI
      Loading required package: ggplot2
      Loading required package: reshape2
      > cuff<-readCufflinks ()
      > cuff
      CuffSet instance with:
      2 samples
      24302 genes
      42262 isoforms
      28828 TSS
      25037 CDS
      24302 promoters
      28828 splicing
      0 relCDS
      > iso.diff <- diffData(isoforms(cuff))
      > iso.diff.top <- iso.diff[order(iso.diff$q_value),][1:20,]
      > iso.diff.top
      isoform_id sample_1 sample_2 status value_1 value_2
      19598 TCONS_00019647 q1 q2 OK 0.00142518 63.8030
      23003 TCONS_00023056 q1 q2 OK 0.01873000 267.5380
      16085 TCONS_00016126 q1 q2 OK 0.00828880 53.7744
      20375 TCONS_00020425 q1 q2 OK 0.01018440 41.0838
      14718 TCONS_00014757 q1 q2 OK 0.01255110 52.7526
      38909 TCONS_00038994 q1 q2 OK 0.00506554 18.4579
      9364 TCONS_00009383 q1 q2 OK 0.01624700 41.5996
      21567 TCONS_00021617 q1 q2 OK 0.02047770 43.5210
      21617 TCONS_00021668 q1 q2 OK 0.07737150 173.5400
      12908 TCONS_00012945 q1 q2 OK 0.01454510 29.1976
      2916 TCONS_00002919 q1 q2 OK 0.02808040 52.5176
      11888 TCONS_00011918 q1 q2 OK 0.01283370 23.4124
      24967 TCONS_00025024 q1 q2 OK 0.07871780 93.7237
      36578 TCONS_00036659 q1 q2 OK 0.15108000 179.3100
      18827 TCONS_00018874 q1 q2 OK 0.19685300 402.2040
      26748 TCONS_00026809 q1 q2 OK 0.07271350 66.3874
      24573 TCONS_00024628 q1 q2 OK 0.01203420 20.7750
      5805 TCONS_00005818 q1 q2 OK 0.00198928 2.9240
      35808 TCONS_00035884 q1 q2 OK 0.10710700 108.1710
      26864 TCONS_00026926 q1 q2 OK 0.05353970 86.0766
      log2_fold_change test_stat p_value q_value significant
      19598 15.45020 -7.91793 2.44249e-15 5.34124e-11 yes
      23003 13.80210 -7.39372 1.42775e-13 1.56110e-09 yes
      16085 12.66350 -7.33093 2.28484e-13 1.66550e-09 yes
      20375 11.97800 -7.27264 3.52607e-13 1.92770e-09 yes
      14718 12.03720 -7.23914 4.51417e-13 1.97432e-09 yes
      38909 11.83120 -7.17187 7.39853e-13 2.69652e-09 yes
      9364 11.32220 -6.84004 7.91722e-12 2.47334e-08 yes
      21567 11.05340 -6.73898 1.59504e-11 3.87558e-08 yes
      21617 11.13120 -6.75063 1.47207e-11 3.87558e-08 yes
      12908 10.97110 -6.67956 2.39653e-11 5.24073e-08 yes
      2916 10.86900 -6.61070 3.82498e-11 6.62383e-08 yes
      11888 10.83310 -6.59542 4.24061e-11 6.62383e-08 yes
      24967 10.21750 -6.60852 3.88183e-11 6.62383e-08 yes
      36578 10.21290 -6.59690 4.19833e-11 6.62383e-08 yes
      18827 10.99660 -6.54690 5.87441e-11 8.56411e-08 yes
      26748 9.83447 -6.44433 1.16116e-10 1.58701e-07 yes
      24573 10.75350 -6.42860 1.28785e-10 1.65663e-07 yes
      5805 10.52150 -6.40323 1.52120e-10 1.84809e-07 yes
      35808 9.98005 -6.39398 1.61620e-10 1.86017e-07 yes
      26864 10.65080 -6.35030 2.14901e-10 2.34972e-07 yes


      however, these top 20 include transcripts that start with NM_00000 and NR_00000

      what I want is to select only the NM_ as these are proteins/transcript, NR_ if I am not wrong is the gene (here cummerbund only gives TCONS, but I have double checked themn with the NM/NR nomenclature and I know they are mixed up as it is listing by fold change...)

      How do I command this on cummerbund?

      thanks,
      ibseq

      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
      17 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      22 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      46 views
      0 likes
      Last Post seqadmin  
      Working...
      X