[BioC] interaction effects for DEXSeq

[Mallon, Eamonn B. (Dr.)]

My initial question still stands, but I have also tried a simpler model by
just looking at the effect of strain on one colony.

So there are two levels to condition (strain = 6 or 8)

It runs fine but I get
> table(res1$padjust < 0.1)

FALSE  TRUE 
65836  5987 


This seems excessive

And the warning (50 times)

> DEXSeqHTML( ecs, FDR=0.1, )
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In chol.default(XVX + lambda * I, pivot = TRUE) :
  the matrix is either rank-deficient or indefinite



Any ideas what is happening

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





On 06/06/2013 15:22, "Mallon, Eamonn B. (Dr.)" <ebm3 at leicester.ac.uk>
wrote:

>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
>
>
>	[[alternative HTML version deleted]]
>
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