Hello, Does anyone know if there is a limited number of levels for a factor or how to reset the defaults? I have a two factor experiment which one factor has 2 levels while another has 7 levels. I got errors while I run following analysis. Please help. Thanks, Steve > design <- model.matrix(~phe+tr) > design (Intercept) pheVehicle tr1-Ant tr2-TCDD tr3-DIM tr4-Ago tr5-CH tr6- DMSO 1 1 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 3 1 0 0 0 0 0 0 0 4 1 1 0 0 0 0 0 1 5 1 1 0 0 0 0 0 1 6 1 1 0 0 0 0 0 1 7 1 1 0 1 0 0 0 0 8 1 1 0 1 0 0 0 0 9 1 1 0 1 0 0 0 0 10 1 1 0 0 1 0 0 0 11 1 1 0 0 1 0 0 0 12 1 1 0 0 1 0 0 0 13 1 1 0 0 0 1 0 0 14 1 1 0 0 0 1 0 0 15 1 1 0 0 0 1 0 0 16 1 1 0 0 0 0 1 0 17 1 1 0 0 0 0 1 0 18 1 1 0 0 0 0 1 0 19 1 1 1 0 0 0 0 0 20 1 1 1 0 0 0 0 0 21 1 1 1 0 0 0 0 0 attr(,"assign") [1] 0 1 2 2 2 2 2 2 attr(,"contrasts") attr(,"contrasts")$phe [1] "contr.treatment" attr(,"contrasts")$tr [1] "contr.treatment" > fit <- lmFit(x.data, design) Coefficients not estimable: tr6-DMSO Warning message: Partial NA coefficients for 29198 probe(s) > fit2 <- eBayes(fit) Warning message: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) : Estimation of var.prior failed - set to default value > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.2.2 loaded via a namespace (and not attached): [1] tools_2.10.1

Hi Steve, On 8/7/2010 2:32 PM, steve shen wrote: > Hello, > > Does anyone know if there is a limited number of levels for a factor or > how to reset the defaults? I have a two factor experiment which one > factor has 2 levels while another has 7 levels. I got errors while I run > following analysis. Please help. Thanks, The limit to the number of factors is dependent on the number of samples you have. In your case, you are fooling R into creating a design matrix that is not of full rank. Anyway, I am not sure you want to use the 'phe' factor. I am guessing that you have some sort of control sample that is not treated, and then six other sample types that are treated with the same thing, but in a different vehicle. In which case I think you just want design <- model.matrix(~tr) which is full rank. The baseline in this case would be the untreated sample, and the coefficients for everything else would be the comparison of the treatment/vehicle combination to the untreated sample. Best, Jim > > Steve > > > design <- model.matrix(~phe+tr) > > design > (Intercept) pheVehicle tr1-Ant tr2-TCDD tr3-DIM tr4-Ago tr5-CH tr6-DMSO > 1 1 0 0 0 0 0 0 0 > 2 1 0 0 0 0 0 0 0 > 3 1 0 0 0 0 0 0 0 > 4 1 1 0 0 0 0 0 1 > 5 1 1 0 0 0 0 0 1 > 6 1 1 0 0 0 0 0 1 > 7 1 1 0 1 0 0 0 0 > 8 1 1 0 1 0 0 0 0 > 9 1 1 0 1 0 0 0 0 > 10 1 1 0 0 1 0 0 0 > 11 1 1 0 0 1 0 0 0 > 12 1 1 0 0 1 0 0 0 > 13 1 1 0 0 0 1 0 0 > 14 1 1 0 0 0 1 0 0 > 15 1 1 0 0 0 1 0 0 > 16 1 1 0 0 0 0 1 0 > 17 1 1 0 0 0 0 1 0 > 18 1 1 0 0 0 0 1 0 > 19 1 1 1 0 0 0 0 0 > 20 1 1 1 0 0 0 0 0 > 21 1 1 1 0 0 0 0 0 > attr(,"assign") > [1] 0 1 2 2 2 2 2 2 > attr(,"contrasts") > attr(,"contrasts")$phe > [1] "contr.treatment" > > attr(,"contrasts")$tr > [1] "contr.treatment" > > > fit <- lmFit(x.data, design) > Coefficients not estimable: tr6-DMSO > Warning message: > Partial NA coefficients for 29198 probe(s) > > fit2 <- eBayes(fit) > Warning message: > In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = > stdev.coef.lim) : > Estimation of var.prior failed - set to default value > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] limma_3.2.2 > > loaded via a namespace (and not attached): > [1] tools_2.10.1 > > _______________________________________________ > 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