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  • Error in microbial count object: Error in hatmatrix/non-conformable arguments

    I imported a phyloseq object to DESEQ2 for obtaining the log2fold change in the number of OTU's per sample. My condition is the disease_stat: cancer, healthy, adenoma

    Following is the code i used:

    phyloseq_to_deseq2(biom_otu_tax, ~disease_stat)
    cts=counts(DESeq2BIOM)
    geoMeans = apply(cts, 1, function(row) if (all(row == 0)) 0 else exp(mean(log(row[row != 0]))))
    DESeq2BIOM = estimateSizeFactors(DESeq2BIOM, geoMeans = geoMeans)
    #It stopped working after this point
    DESeq2BIOM = estimateDispersions(DESeq2BIOM)
    DESeq2BIOMRES = DESeq(DESeq2BIOM,test = "Wald", betaPrior = "FALSE")
    DESeq2BIOMRES = DESeq(DESeq2BIOM,test = "Wald")

    The error I get is Error in t(hatmatrix %*% t(y)) :
    "error in evaluating the argument 'x' in selecting a method for function 't': Error in hatmatrix %*% t(y) : non-conformable arguments"

    I browsed a few other solutions before posting a question: http://seqanswers.com/forums/archive...p/t-46009.html
    They did not address my issue.

    What does this error indicate? Help in troubleshooting much appreciated!

  • #2
    I moved this to Bioinformatics where you'll have better luck.

    Comment


    • #3
      Error in hatmatrix %*% t(y) : non-conformable arguments"

      Thanks for moving it here. New to the community and would appreciate some direction to troubleshoot the issue!

      Comment


      • #4
        What version of DESeq2 software are you using? Type: sessionInfo(). The latest release is 1.8, so I'd recommend first checking if updating helps.

        Note that DESeq() includes estimateDispersions() as a step, so you can just proceed from your custom size factor calculation to DESeq().

        Comment


        • #5
          Hello,

          I happen to have a similar problem to what the original poster had:

          > DiffAbund <- DESeq(DiffAbund, test="Wald", fitType="parametric")
          estimating size factors
          estimating dispersions
          gene-wise dispersion estimates
          Error in t(hatmatrix %*% t(y)) :
          error in evaluating the argument 'x' in selecting a method for function 't': Error in hatmatrix %*% t(y) : non-conformable arguments



          The DESeq2 version I'm running is 1.8.2.

          Any suggestions on what might be the problem and how to solve it? I have a bunch of variables in the model, so I guess taking a few out could solve the issue with the matrix operations, but I'm trying to avoid that. Any help would be very mucho appreciated.

          Comment


          • #6
            I know this is an old thread, but in my case the error was because I had collapsed technical replicates

            Comment

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