Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq Plot Error

    Hi,

    I'm trying to plot the scatterplot of direct vs. moderated log-ratios and I keep getting an error:

    Error in plot.window(...) : need finite 'ylim' values
    In addition: Warning messages:
    1: In min(x) : no non-missing arguments to min; returning Inf
    2: In max(x) : no non-missing arguments to max; returning -Inf

    This is what I have put in:

    > cdsBlind <- estimateDispersions( cds, method="blind" )
    > vsd <- getVarianceStabilizedData( cdsBlind )
    > mod_lfc <- (rowMeans( vsd[, conditions(cds)=="treated", drop=FALSE] ) -
    + rowMeans( vsd[, conditions(cds)=="untreated", drop=FALSE] ))
    > lfc <- res$log2FoldChange
    > finite <- is.finite(lfc)
    > table(as.character(lfc[!finite]), useNA="always")

    -Inf Inf NaN <NA>
    83 212 285 0
    > largeNumber <- 10
    > lfc <- ifelse(finite, lfc, sign(lfc) * largeNumber)
    > plot( lfc, mod_lfc, pch=20, cex=.3,
    + col = ifelse( finite, "#80808040", "red" ) )

    Is it because I am running analysis on samples with no replicates? (I know - not good, but it's all that I have...). Any ideas? Thanks.

  • #2
    Dear Coral Girl

    it looks like your mod_lfc consists of all non-finite values. What are the conditions names in your object cds? Note that in the line

    mod_lfc <- (
    rowMeans( vsd[, conditions(cds)=="treated", drop=FALSE] ) -
    rowMeans( vsd[, conditions(cds)=="untreated", drop=FALSE] ))
    you select columns in the data matrix with the names treated and untreated, and if there are no such columns, rowMeans will return NaN. In this case, you need to modify the above code according to your condition names.

    Hope this helps.
    Wolfgang
    Wolfgang Huber
    EMBL

    Comment


    • #3
      Hi Wolfgang,

      Thank you very much - that was exactly the problem. A rookie mistake on my behalf!

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