DEXSeq and formuladispersions error

[ega2d]

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.

[Simon Anders]

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.