Dear all
I have 11 samples for a cross infection experiment where there are two colonies (the hosts K or Q) and 2 strains (6 or 8).

sample colony strain type
K61 k six single-read
K62 k six single-read
K63 k six single-read
K81 k eight single-read
K82 k eight single-read
K83 k eight single-read
Q61 q six single-read
Q62 q six single-read
Q63 q six single-read
Q81 q eight single-read
Q82 q eight single-read

I am most interested in finding exon usage differences related to the interaction of the colony and strain factors. Following the vignette I put the following code together


formuladispersion<-count~sample+(colony:strain)+exon
ecs<-estimateDispersions(ecs, formula=formuladispersion)
ecs<-fitDispersionFunction(ecs)

formula0<-count~sample+exon+(colony:strain)
formula1<-count~sample+exon+(colony:strain)*I(exon==exonID)
ecs<-testForDEU(ecs, formula0=formula0, formula1=formula1)

Does this make sense?

Thanks in advance
Eamonn

Dr Eamonn Mallon
Lecturer in Evolutionary Biology
Adrian 220
Biology Department
University of Leicester

http://www2.le.ac.uk/departments/biology/people/mallon


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