Hi Juan, James it does seem strange that this warning should occur for such an experimental design. I would advise to spend a bit of time on data quality control (the arrayQualityMetrics package is a good start), just to make sure that there are no problems such as duplicate files, inappropriate preprocessing, etc. Supposing that your 'intensity' object is a matrix, how does this look like? library("vsn") meanSdPlot(intensity) library("genefilter") rt = rowttests(intensity, fac=factor(TS)) hist(rt$p.value, breaks=50) (I couldn't test this code on your data object, so adaptations might be needed.) Best wishes Wolfgang James W. MacDonald scripsit 01/15/2010 03:15 PM: > 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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact