Hi Adam, Adam Kiezun wrote: > Dear Wei, > Thank you for your response. The design you propose is in fact exactly > what I use right now. I agree with Michael though - I think I need to > explicitly indicate to limma that my replicates are technical. In the > manual, the duplicateCorrelation function is used for this purpose in > a two-channel array. My question is then how to use > duplicateCorrelation in a single-channel analysis. This is outlined in both the Limma User's Guide, and the help page for duplicateCorrelation(). From ?duplicateCorrelation: Details: When 'block=NULL', this function estimates the correlation between duplicate spots (regularly spaced within-array replicate spots). If 'block' is not null, this function estimates the correlation between repeated observations on the blocking variable. Typically the blocks are biological replicates and the repeated observations are technical replicates. so dupcor <- duplicateCorrelation(x, design, block=rep(1:3, each = 2)) should be what you want. Best, Jim > > ./adam > > On Thu, Mar 25, 2010 at 6:37 PM, Wei Shi <shi at="" wehi.edu.au=""> wrote: >> Dear Adam: >> >> You can use the following commands to create a design matrix for your >> experiment: >> >> s <- factor(c("A","A","B","B","C","C")) >> design <- model.matrix(~0+s) >> colnames(design) <- levels(s) >> fit <- lmFit(x,design) >> >> To do a pairwise comparison, you can use the makeConstrasts function: >> >> contr <- makeContrasts(A-B,A-C,B-C,levels=design) >> fit.contr <- eBayes(contrasts.fit(fit,contr)) >> >> Cheers, >> Wei >> >> Adam Kiezun wrote: >>> Hi, >>> How do I write the design matrix to specify technical replicates in >>> multi-group experiment on a single-channel array (data coming from >>> lumi)? >>> >>> I have 3 groups of samples (A, B, C), each group has 2 technical >>> replicates (so I have 6 expression vectors: A1, A2, B1, B2, B3). How >>> do I write the design matrix to tell limma that A1 and A2 etc are >>> technical replicates and that I want to do all pairwise comparisons >>> between groups (ie. AvsB, AvsC, BvsC)? >>> >>> The limma manual covers technical replicates for two-channel arrays, >>> and the multi-group experiments with biological replicates. I'd like >>> to know how to deal with a one-channel arrays, multi-group experiment >>> with technical replicates. >>> >>> regards >>> Adam >>> >>> _______________________________________________ >>> 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 >>> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> > > _______________________________________________ > 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