[BioC] interaction effects for DEXSeq

[Mallon, Eamonn B. (Dr.)]

Can any one help with the below?
Dr Eamonn Mallon
Lecturer in Evolutionary Biology
Adrian 220
Biology Department
University of Leicester

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





On 07/06/2013 14:30, "Mallon, Eamonn B. (Dr.)" <ebm3 at mail.cfs.le.ac.uk>
wrote:

>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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>