[BioC] limma, duplicateCorrelation, dupfit$consensus = 1: concerning?

[Karl Brand]

I see now that i can not proceed with such a design including 
duplicateCorrelation (output below).  Perhaps it results from trying to 
do to much with too few observations/replicates.

I'd still really like to hear explanations why this might be so.

cheers,

Karl

 >      fit <- lmFit(rma.pp, design, correlation=dupfit$consensus, 
block=Animal)
Error in chol.default(V) :
   the leading minor of order 2 is not positive definite
 >

On 5/24/2010 3:18 PM, Karl Brand wrote:
> Dear BioC,
>
> I'm attempting to use the duplicateCorrelation function within limma to
> control for fact that tissues being studied come from the same animals.
> I understand that for this work appropriately, dupfit$consensus needs to
> be positive, which at "1", it is.
>
> But such an exact value is concerning to my inexperienced eye.
>
> I'd greatly appreciate hearing from people with experience using
> duplicateCorrelation what this outcome represents and if indeed is
> something to be wary of and perhaps omitted.
>
> With thanks in advance,
>
> cheers,
>
> Karl
>
>> design <- model.matrix(~Time * Pperiod * Tissue - Time : Pperiod :
> Tissue)
>> source(.trPaths[5], echo=TRUE, max.deparse.length=150)
>
>> dupfit <- duplicateCorrelation(rma.pp, design, ndups=1, block=Animal)
>
>> dupfit$consensus #remembering to check that dupfit$consensus is
> positive.
> [1] 1
> There were 50 or more warnings (use warnings() to see the first 50)
>> warnings()
> Warning messages:
> 1: In sqrt(dfitted.values) : NaNs produced
> 2: In sqrt(dfitted.values) : NaNs produced
> 3: In sqrt(dfitted.values) : NaNs produced
> 4: In sqrt(dfitted.values) : NaNs produced
> 5: In sqrt(dfitted.values) : NaNs produced
> 6: In sqrt(dfitted.values) : NaNs produced
> 7: In sqrt(dfitted.values) : NaNs produced
> 8: In sqrt(dfitted.values) : NaNs produced
> 9: In sqrt(dfitted.values) : NaNs produced
> 10: In sqrt(dfitted.values) : NaNs produced
> 11: In sqrt(dfitted.values) : NaNs produced
> 12: In sqrt(dfitted.values) : NaNs produced
> 13: In sqrt(dfitted.values) : NaNs produced
> 14: In sqrt(dfitted.values) : NaNs produced
> 15: In sqrt(dfitted.values) : NaNs produced
> 16: In sqrt(dfitted.values) : NaNs produced
> 17: In sqrt(dfitted.values) : NaNs produced
> 18: In sqrt(dfitted.values) : NaNs produced
> 19: In sqrt(dfitted.values) : NaNs produced
> 20: In sqrt(dfitted.values) : NaNs produced
> 21: In sqrt(dfitted.values) : NaNs produced
> 22: In sqrt(dfitted.values) : NaNs produced
> 23: In sqrt(dfitted.values) : NaNs produced
> 24: In sqrt(dfitted.values) : NaNs produced
> 25: In sqrt(dfitted.values) : NaNs produced
> 26: In sqrt(dfitted.values) : NaNs produced
> 27: In sqrt(dfitted.values) : NaNs produced
> 28: In sqrt(dfitted.values) : NaNs produced
> 29: In sqrt(dfitted.values) : NaNs produced
> 30: In sqrt(dfitted.values) : NaNs produced
> 31: In sqrt(dfitted.values) : NaNs produced
> 32: In sqrt(dfitted.values) : NaNs produced
> 33: In sqrt(dfitted.values) : NaNs produced
> 34: In sqrt(dfitted.values) : NaNs produced
> 35: In sqrt(dfitted.values) : NaNs produced
> 36: In sqrt(dfitted.values) : NaNs produced
> 37: In sqrt(dfitted.values) : NaNs produced
> 38: In sqrt(dfitted.values) : NaNs produced
> 39: In sqrt(dfitted.values) : NaNs produced
> 40: In sqrt(dfitted.values) : NaNs produced
> 41: In sqrt(dfitted.values) : NaNs produced
> 42: In sqrt(dfitted.values) : NaNs produced
> 43: In sqrt(dfitted.values) : NaNs produced
> 44: In sqrt(dfitted.values) : NaNs produced
> 45: In sqrt(dfitted.values) : NaNs produced
> 46: In sqrt(dfitted.values) : NaNs produced
> 47: In sqrt(dfitted.values) : NaNs produced
> 48: In sqrt(dfitted.values) : NaNs produced
> 49: In sqrt(dfitted.values) : NaNs produced
> 50: In sqrt(dfitted.values) : NaNs produced
>>
>
>
>

-- 
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3457 | F +31 (0)10 704 4743 | M +31 (0)642 777 268