Error messages from eBayes()(limma)
1
0
Entering edit mode
@julinaecomyuedu-1967
Last seen 9.6 years ago
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 [[alternative HTML version deleted]]
Microarray Microarray • 2.5k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 51 minutes ago
United States
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 -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENT
0
Entering edit mode
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
ADD REPLY

Login before adding your answer.

Traffic: 930 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6