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  • areyes
    replied
    dispersion columns in DEXSeq

    Hi,

    I think I did not understand exactly what you want to do with your simulations, but the way DEXSeq stores the dispersion parameters is the following (demonstrated in the pasilla data package):

    Code:
    data("pasillaExons", package="pasilla")
    pasillaExons <- fitDispersionFunction(estimateDispersions( estimateSizeFactors( pasillaExons ) ))
    fData(pasillaExons)$dispBeforeSharing
    [email protected]
    fData(pasillaExons)$dispFitted
    fData(pasillaExons)$dispersion
    after calling estimateDispersions and fitDispersionFunction, dispBeforeSharing will contain the Cox-Reid dispersion estimates, dispFitted will contain the mean-variance fitted values for the exons respective count value ([email protected] contains the information from the function itself), and the dispersion column will contain the maximum between the two previous and this last is the one use for testing. I guess you could modify this last column for your simulations... but, what exactly you want to see when you simulate this dispersion values?

    Leave a comment:


  • Pedrissimo
    started a topic dexseq simulation

    dexseq simulation

    Hello,

    I am comparing two drug treated samples to two control samples, both are biological replicates. I'd like to test how different levels of dispersion effect my samples by varying the level of dispersion for each sample. How can I assign different artificial dispersion levels to each pair of biological replicates?
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