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  • How to use DESeq with non Integer values from mirdeep2

    Hi,

    I've recently started using mirdeep2 for miRNAseq data and would like to do a DE analysis between two conditions.

    The normalised miRNA expressions were given in an output file by mirdeep2 called "miRNAs_expressed_all_samples_now.csv" which contained colums like this:

    #miRNA read_count precursor total seq seq(norm)
    mmu-let-7a-1-3p 571.00 mmu-let-7a-1 571.00 571.00 74.79
    mmu-let-7a-5p 38731.00 mmu-let-7a-1 38731.00 38731.00 5073.08

    The colum with my normalised scores (seq(norm)) has non integer values which I have been unable to use with DESeq to perform a DE analysis.

    I was given the following error when i tried to attatch my conditions to the counts table.
    > cds<-newCountDataSet(countsTable, conds)
    Error in newCountDataSet(countsTable, conds) :
    The countData is not integer.

    Has anyone come across this before? Should i convert my seq(norm) colum to integer values or is there a way to force DESeq to accept non integer values.

    Any help or advice you can give would be much appriciate.

  • #2
    When I went through the mirdeep2 to DESeq, I just used the raw counts as output by mirdeep2 and not the mideep2 normalized counts. DESeq will normalize for you anyway.

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    • #3
      Excellent! That worked like a charm.

      Cheers

      Comment


      • #4
        Originally posted by Wallysb01 View Post
        When I went through the mirdeep2 to DESeq, I just used the raw counts as output by mirdeep2 and not the mideep2 normalized counts. DESeq will normalize for you anyway.
        Hi, Wallysb01, if I use -W in quantifier.pl options which you mentioned in another thread then the raw counts will have non-integer numbers. How to deal with this situation? Is that appropriate to use function 'round' in R to convert these numbers to integer?
        Thanks~

        Comment

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