[R-sig-ME] Dimension error message when using lmer()

[ONKELINX, Thierry]

Dear Doug,

Since logRatioAverage is not a factor you get a random effect for each
levels. Hence you end up with more random effects than you can estimate
on the data. 

I suppose that you want a random intercept and a random slope along
logRatioAverage for each array. In that case the model looks like:

lmer(fittedResidual ~ logRatioAverage + logRatioAverage:condition +
(logRatioAverage|array)

HTH,

Thierry
------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
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tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be

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say what the experiment died of.
~ Sir Ronald Aylmer Fisher

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~ Roger Brinner

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ensure that a reasonable answer can be extracted from a given body of
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-----Oorspronkelijk bericht-----
Van: r-sig-mixed-models-bounces at r-project.org
[mailto:r-sig-mixed-models-bounces at r-project.org] Namens Doug Fowler
Verzonden: woensdag 25 november 2009 23:40
Aan: r-sig-mixed-models at r-project.org
Onderwerp: [R-sig-ME] Dimension error message when using lmer()

Dear list,

I am quite new to R and linear mixed models, and am struggling to fit
some microarray data.  Here is what I am trying to do:

lmer(fittedResidual ~ logRatioAverage + logRatioAverage:condition + (1|
logRatioAverage:array)

on the data set (also attached as a text file, if that helps):

         array condition systematicName logRatioAverage         
fittedresid     fittedResidual
6730   090409     Cond1        YHR055C      1.39287821    
1.38727125276748   1.38727125276748
7171   090909     Cond4        YHR055C     1.164289223    
1.15424383373922   1.15424383373922
7825   090909     Cond1        YHR055C     1.453747825    
1.44370243573922   1.44370243573922
12055  090409     Cond3        YHR055C      1.04792081    
1.04231385276748   1.04231385276748
25611  090409     Cond2        YHR055C   -0.4305436158  
-0.436150573032517 -0.436150573032517
26799  090909     Cond3        YHR055C     1.223053989    
1.21300859973922   1.21300859973922
51051  090409     Cond5        YHR055C   -0.6111279389  
-0.616734896132517 -0.616734896132517
56939  092909     Cond5        YHR055C   -0.3191377724  
-0.328468510731881 -0.328468510731881
79176  090909     Cond5        YHR055C   -0.3398805279  
-0.349925917160780 -0.349925917160780
87437  092909     Cond2        YHR055C   -0.2774113157  
-0.286742054031881 -0.286742054031881
93622  092909     Cond1        YHR055C    0.4629267583   
0.453596019968119  0.453596019968119
100011 092909     Cond6        YHR055C    0.2566897012   
0.247358962868119  0.247358962868119
100588 092909     Cond4        YHR055C     0.300567509   
0.291236770668119  0.291236770668119
105792 092909     Cond3        YHR055C    0.5033090594   
0.493978321068119  0.493978321068119
105796 090909     Cond2        YHR055C   -0.2170950589  
-0.227140448160780 -0.227140448160780
106182 090909     Cond6        YHR055C    0.8978423582    
0.88779696893922   0.88779696893922
107145 090409     Cond4        YHR055C     1.096596091    
1.09098913376748   1.09098913376748
18     090409     Cond6        YHR055C              NA                  
NA                 NA

produces the errors and warnings:

Error in validObject(.Object) :
   invalid class "mer" object: Slot Zt must by dims['q']  by
dims['n']*dims['s'] In addition: Warning messages:
1: In logRatioAverage:array :
   numerical expression has 17 elements: only the first used
2: In logRatioAverage:array :
   numerical expression has 17 elements: only the first used

Any help diagnosing what I'm doing wrong or even advice about where some
good resources are to be found would be greatly appreciated!

Thanks,

Doug

Douglas M. Fowler, Ph. D.
Department of Genome Sciences
University of Washington
dfowler at u.washington.edu



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