Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Warnings using Galaxy and local CummeRbund

    Hello everyone,

    Using Galaxy and a reference genome, I have run the TopHat>Cufflinks>Cuffdiff pipeline on 12 single-end Illumina RNA-seq samples (one control condition and three treatments, 3 biological replicates each).

    I have content in the outputs from galaxy so that I can see clearly log fold changes, p-values, accession/transcript name, and so on.

    I downloaded all of the output files and changed the names according to the table below and attempted to run it in cummeRbund (in Rstudio) using the command:

    > cuff_data<-readCufflinks('C:/Users/me/Documents/RNA-seq/CuffDiff Output')

    and I receive the following warnings:

    1: RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier().
    2: Column name mismatch, columns will be matched by position. This warning may be converted to an error soon.
    3: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
    4: attributes are not identical across measure variables; they will be dropped
    5: Named parameters not used in query: log2.fold_change.
    6: Named parameters not used in query: gene_id, sample_1, sample_2, status, value_1, value_2, sqrt.JS., test_stat, p_value, q_value, significant
    7: Named parameters not used in query: tracking_id, gene_id, CDS_id, gene_short_name, tss_id, class_code, nearest_ref_id, locus, length, coverage
    8: attributes are not identical across measure variables; they will be dropped
    9: Named parameters not used in query: tracking_id, sample_name, fpkm, conf_hi, conf_lo, status
    10: Named parameters not used in query: test_id, sample_1, sample_2, status, value_1, value_2, log2.fold_change., test_stat, p_value, q_value, significant
    11: Named parameters not used in query: tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, locus, length, coverage
    12: attributes are not identical across measure variables; they will be dropped
    13: Named parameters not used in query: tracking_id, sample_name, fpkm, conf_hi, conf_lo, status
    14: Named parameters not used in query: test_id, sample_1, sample_2, status, value_1, value_2, log2.fold_change., test_stat, p_value, q_value, significant
    15: Named parameters not used in query: test_id, gene_id, sample_1, sample_2, status, value_1, value_2, sqrt.JS., test_stat, p_value, q_value, significant

    Does anybody know if it's possible to use the Galaxy data output to use cummeRbund locally? This would be preferred to using cummeRbund in Galaxy. I am using Windows 10, and the latest versions of both Rstudio and cummeRbund. SQLite confuses me, but I think I have the latest version since I have installed the package RSQLite using the Rstudio software manager.

    Any help would go a long ways and be greatly appreciated. Thank you for your time.
    -A
    Attached Files

  • #2
    Same error

    I jsut got that same error, were you able to figure out how to solve it? I am using Windows 7, and just re-installed the latest R and cummerbund

    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
    57 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