Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Help Using DESeq without replicates

    Hello,

    I'm working with a data set that we have yet to replicate. I'm trying to take a cursory look at the differential expression, but I keep getting an error I don't understand. I don't know if it matters but I'm generating my count tables with HTSeq. Here is the error:

    > table = read.delim(file="~/neuron_rna_seq/hypodermis_table.txt", header=FALSE, stringsAsFactors=TRUE)
    > cds = newCountDataSetFromHTSeqCount(table, directory="~/neuron_rna_seq")
    > cds = estimateSizeFactors( cds )
    > sizeFactors( cds )
    hypodermis hypodermis_unfiltered
    0.3333333 3.0000000
    > cds = estimateDispersions(cds, method="blind", sharingMode="fit-only")
    Error in parametricDispersionFit(means, disps) :
    Parametric dispersion fit failed. Try a local fit and/or a pooled estimation. (See '?estimateDispersions')
    In addition: Warning message:
    glm.fit: algorithm did not converge
    #Because of this I use the local fit
    > cds = estimateDispersions(cds, method="blind", sharingMode="fit-only", fitType="local")
    > results = nbinomTest(cds, "hypodermis", "hypodermis_unfiltered")
    #Error in question
    Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] == :
    missing value where TRUE/FALSE needed


    I apologize if this is a basic question, I'm not an experienced user.

    Thanks!
    April

  • #2
    Answer to my own question

    Hi All,

    Figures the first time I post a question I end up answering it myself.

    My conditions were not named what I thought they were. I solved this by using dispTable(cds)[CondA]. With the incorrect condition name this evaluated to NA, thus causing the error.

    Sorry for the stupid question, maybe this will help a similarly misguided person!

    Comment


    • #3
      It was useful, thanks!

      Comment


      • #4
        raju

        Originally posted by aprilw View Post
        Hello,

        I'm working with a data set that we have yet to replicate. I'm trying to take a cursory look at the differential expression, but I keep getting an error I don't understand. I don't know if it matters but I'm generating my count tables with HTSeq. Here is the error:

        > table = read.delim(file="~/neuron_rna_seq/hypodermis_table.txt", header=FALSE, stringsAsFactors=TRUE)
        > cds = newCountDataSetFromHTSeqCount(table, directory="~/neuron_rna_seq")
        > cds = estimateSizeFactors( cds )
        > sizeFactors( cds )
        hypodermis hypodermis_unfiltered
        0.3333333 3.0000000
        > cds = estimateDispersions(cds, method="blind", sharingMode="fit-only")
        Error in parametricDispersionFit(means, disps) :
        Parametric dispersion fit failed. Try a local fit and/or a pooled estimation. (See '?estimateDispersions')
        In addition: Warning message:
        glm.fit: algorithm did not converge
        #Because of this I use the local fit
        > cds = estimateDispersions(cds, method="blind", sharingMode="fit-only", fitType="local")
        > results = nbinomTest(cds, "hypodermis", "hypodermis_unfiltered")
        #Error in question
        Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] == :
        missing value where TRUE/FALSE needed


        I apologize if this is a basic question, I'm not an experienced user.

        Thanks!
        April
        Useful
        Thank you

        Comment


        • #5
          I have the same error … but I did not understand how solve it, can you help me?

          Comment


          • #6
            My pipeline in DEseq using data without replicates and 2 conditions is not working either. I thought that something was wrong with the dispersion. But no dispersion method works, so...maybe there's a problem with the preprocessing? Anybody got the same problem with DESeq?

            Comment


            • #7
              Hi April,

              What exactly did you do with dispTable(cds)[CondA]?

              Thanks.

              Originally posted by aprilw View Post
              Hi All,

              Figures the first time I post a question I end up answering it myself.

              My conditions were not named what I thought they were. I solved this by using dispTable(cds)[CondA]. With the incorrect condition name this evaluated to NA, thus causing the error.

              Sorry for the stupid question, maybe this will help a similarly misguided person!

              Comment

              Latest Articles

              Collapse

              • seqadmin
                The Impact of AI in Genomic Medicine
                by seqadmin



                Article Coming Soon......
                Today, 02:07 PM
              • seqadmin
                Multiomics Techniques Advancing Disease Research
                by seqadmin


                New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

                A major leap in the field has
                ...
                02-08-2024, 06:33 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 02-23-2024, 04:11 PM
              0 responses
              31 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 02-21-2024, 08:52 AM
              0 responses
              45 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 02-20-2024, 08:57 AM
              0 responses
              36 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 02-14-2024, 09:19 AM
              0 responses
              63 views
              0 likes
              Last Post seqadmin  
              Working...
              X