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

-- 
---------------------------------------------------------------------
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden
Germany

http://people.mpi-cbg.de/domingue/home.html
e-mail: domingue@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology


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