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  • DEXSeq and formuladispersions error

    Hi all,

    I'm having some trouble with the portion of 'estimateDispersions' of DEXSeq. It worked when I didn't add in the formuladispersion part of the command, but when I add it in, it gives the following error:

    > ecs <- estimateDispersions(ecs, formula = formuladispersion, maxExon = 250, quiet = FALSE)

    Dispersion estimation. (Progress report: one dot per 100 genes)
    Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
    contrasts can be applied only to factors with 2 or more levels


    Here are more details about my experimental set up:

    > design(ecs)
    condition replicate type
    L1 Fetal 1 paired-end
    L2 Fetal 2 paired-end
    L3 Fetal 3 paired-end
    J4 Adolescent 1 paired-end
    J6 Adolescent 2 paired-end
    J8 Adolescent 3 paired-end
    A5 Adult 1 paired-end
    A6 Adult 2 paired-end
    A7 Adult 3 paired-end

    > formuladispersion
    count ~ sample + (exon + type) * condition

    Any suggestions, clarifications, or links would be greatly appreciated.

  • #2
    If all your library are paired-end, you do not need a factor 'type' for this. Remove it and use the default values for the formulae.

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