[BioC] Study design in DEXSeq

[Alejandro Reyes]

Dear Antonio Domingues,

It is not possible to modify the DEXSeq formulas in order to test for 
'not changes in exon usage'.  An option would be to subset your 
ExonCountSet object leaving only the subcellular fractions or the totals 
and do the vanilla DEXSeq analysis in both subsets separately. 
Afterwards you could compare the results by plotting the fold changes 
and try to identify abrupt changes in the knockdown effect differences 
between the cellular fractions and in the total.

Alejandro

> ** I have sent this message before, but somethign must have gone wrong
> because it seems like it never reached the mailing-list. If it did and
> did his a duplicate, my apologies **
>
> Dear Bioconductors,
>
> I would like to ask for some advice/suggestions on the set-up of DEXSeq
> with multiple condictions. At the moment, I am using DEXSeq in a
> "vanilla" fashion:
> - 2 conditions, knockdown and control
> - 2 biological replicates per condition
> - output exons that change upon knockdown.
>
> So far this is working fine. But I also have another experimental
> variable: sub-cellular fractions (total vs fraction). The goal is obtain
> exons whose expression is changed in the knockdown but only in the
> fraction, that is a combined effect of knockdown and sub-cellular
> localization. Following the vignette, I was thinking of an experimental
> design like this:
>               condition      type
> sample1_a    control      total
> sample1_b    control      total
> sample2_a    knockdown    total
> sample2_b    knockdown total
> sample3_a    control      fraction
> sample3_b    control      fraction
> sample4_a    knockdown    fraction
> sample4_b    knockdown    fraction
>
> and the code would be:
> formuladispersion <- count ~ sample + ( condition + type ) * exon
> ecs <- estimateDispersions( ecs, formula = formuladispersion )
> ecs <- fitDispersionFunction(ecs)
> formula0 <- count ~ sample + type * exon + condition
> formula1 <- count ~ sample + type * exon + condition * I(exon == exonID)
> ecs <- testForDEU( ecs, formula0=formula0, formula1=formula1 )
> res2 <- DEUresultTable( ecs )
>
> would this work and is this design correct?
>
> Thank you,
> António
>
>
>
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