Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problem with DESeq2 replaceOutliersWithTrimmedMean

    Hi there,

    I am currently using DESeq2 and have found some NA values in the p-values. From previous post, it was suggested that it is because of a 0 counts in all sample (therefore missing) and because of the Cook's filtering. In the previous version of DESeq2, we can switch off the filtering using nbinomWaldTest(dds, cooksCutoff=FALSE) and this function was gone it the current version. Upon reading the manual, I was found that I can use the function: replaceOutliersWithTrimmedMean to try and get a p-value instead of NA out of DESeq2. However, I've got the following error message:

    Error in matrix(rep(trimBaseMean, ncol(dds)), ncol = dds) :
    non-numeric matrix extent


    Will it has something to do with the warning message I've got from estimateDispersions(dds)?

    gene-wise dispersion estimates
    mean-dispersion relationship
    final dispersion estimates
    Warning messages:
    1: In log(ifelse(y == 0, 1, y/mu)) : NaNs produced
    2: step size truncated due to divergence

    (I have also applied the cqn normalization to my data.)

    Thank you.


    My session information
    R version 3.0.2 (2013-09-25)
    Platform: x86_64-unknown-linux-gnu (64-bit)

    attached base packages:
    [1] parallel splines stats graphics grDevices utils datasets
    [8] methods base

    other attached packages:
    [1] SPIA_2.14.0 KEGGgraph_1.20.0 graph_1.40.1
    [4] XML_3.98-1.1 edgeR_3.4.2 limma_3.18.7
    [7] DESeq2_1.2.8 RcppArmadillo_0.4.000 Rcpp_0.10.6
    [10] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6
    [13] BiocGenerics_0.8.0 cqn_1.8.0 quantreg_5.05
    [16] SparseM_1.03 preprocessCore_1.24.0 nor1mix_1.1-4
    [19] mclust_4.2

    loaded via a namespace (and not attached):
    [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0
    [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2
    [7] lattice_0.20-24 locfit_1.5-9.1 RColorBrewer_1.0-5
    [10] RSQLite_0.11.4 stats4_3.0.2 survival_2.37-4
    [13] tools_3.0.2 xtable_1.7-1

  • #2
    hi,

    Thanks for reporting this. This looks like a simple bug to fix. I will test this and if possible push a new release today.

    Mike

    Comment


    • #3
      Thank you Michael, looking forward to the update

      Comment


      • #4
        I was able to reproduce, and then fix, this bug. I pushed this fix to v1.2.9 now. It should appear in 1-2 days on Bioc.

        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
        49 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