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

 

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

 

 


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