[BioC] Error messages from eBayes()(limma)

[James W. MacDonald]

Hi Juan,

Juan Lin wrote:
> Dear All,
> 
> 1.       I am working on a microarray dataset. The array platform is
> GeneChip Mouse Gene 1.0 ST Array. The experiment design is very straight
> forward: two groups comparison--control vs. treatment, with three chips in
> each group.
> 
> 2.        
> 
> 3.       Below is my code:
> 
>> library(limma)
> 
>> TS<-c("Control","Control","Control","Trt","Trt","Trt")
> 
>> TS<-factor(TS,levels=c("Control","Trt"))
> 
>> design<-model.matrix(~0+TS)
> 
>> colnames(design)<-levels(TS)
> 
>> fit<-lmFit(intensity,design)
> 
>> contrast.matrix<-makeContrasts(TrtvsControl=Trt-Control,levels=design)
> 
>> fit2<-contrasts.fit(fit,contrast.matrix)
> 
>  
> 
> Everything was going well before I tried to use the eBayes function. I got
> the following error:
> 
>  
> 
>> fit2<-eBayes(fit2)
> 
> Warning message:
> 
> In ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
> 
>   Estimation of var.prior failed - set to default value

That's not an error. It's a warning stating that the prior variance 
estimate couldn't be estimated, so you are using the default value.

In other words, the function ran, and gave you results, but one of the 
parameters that is usually estimated from the data was not estimable, so 
you used a default value.

In contrast, an error would result in the function halting without 
returning anything, possibly followed by a big grinding noise, smoke and 
sparks. Or is that just my computer? ;-D

Best,

Jim


> 
>  
> 
> Anybody has idea about the reason for the error? I tried looking up the
> bioconductor archives, but couldn't find any reply that could help solve my
> problem.
>  
> I am using R.2.10.1. 
>  
>> sessionInfo()
> R version 2.10.1 (2009-12-14) 
> i386-pc-mingw32 
>  
> locale:
> [1] LC_COLLATE=English_United States.1252 
> [2] LC_CTYPE=English_United States.1252   
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                          
> [5] LC_TIME=English_United States.1252    
>  
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>  
> other attached packages:
> [1] limma_3.2.1
>  
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
> 
>  
> 
> Many thanks!
> 
> Juan
> 
>  
> 
> -----------------------------
> 
> Juan Lin
> 
> Faculty Associate
> 
> Department of Epidemiology and Population Health
> 
> Albert Einstein College of Medicine
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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