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

[Karl Brand]

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