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  • How do you specifiy specific replicates in DESeq?

    I have three replicates that I made a count table for, with 6 conditions each. I am wondering how I can tell DESeq to only compare data between two replicates as opposed to accounting for all three.

    Naively I can just filter out the correct columns in the count table, but I am thinking there has to be a one-liner in DESeq that would do this for me.

    Thanks.

  • #2
    I think i figured it out:

    Look at the vingette for DESeq and see how they filtered the replicates for a specfic property in the line:

    > pairedSamples = pasillaDesign$libType == "paired-end"

    So, all you would have to do is make a new array in your design table (called pasillaDesign in the vignette) that has binary values (I used 0 for "this replicate is not in the subset of replicates I want", and 1 for "this replicate is in the subset of replicates I want").

    Suppose this aforementioned array was called subset, then all you do is:

    > pairedSamples = pasillaDesign$subset == "1"

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