Hi James, Thanks a lot. I got it. Yours sincerely, Jianhong Ou LRB 710 Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 4/10/13 9:47 AM, "James W. MacDonald" <jmacdon at="" uw.edu=""> wrote: >Hi Jainhong Ou, > >On 4/10/2013 9:24 AM, Ou, Jianhong wrote: >> Hi All, >> >> I have samples like this: >> Targets.txt>> >> Filename group replicates >> V1 vec rep1 >> V2 vec rep2 >> V3 vec rep3 >> A1 aec rep1 >> A2 aec rep2 >> A2 aec rep2 >> C1 cec rep1 >> C2 cec rep2 >> C3 cec rep3 >> D1 dec rep1 >> D2 dec rep2 >> D3 dec rep3 >> E1 eec rep1 >> E2 eec rep2 >> E3 eec rep3 >> >> If I want to compare group vec to all the others, is this correct I >>create model matrix and make contrasts like this, >> design<- model.matrix(~-1+group) >> colnames(design)<- gsub("^group","",colnames(design)) >> contrast.matrix<- makeContrasts(contrasts="vec-(aec+cec+dec+eec)/4", >>levels=design) > >That would be the conventional way of doing it. > >> >> Or should I do it like, >> block<- factor(c(rep("b1", 3), rep("b2",12))) >> design<- model.matrix(~-1+block+block:group) >> colnames(design)<- gsub("^block","",colnames(design)) >> contrast.matrix<- makeContrasts(contrasts="b1-b2", levels=design) > >That would not be a way to do it. Did you look at the design matrix you >created? If so did you notice that you have four columns that contain >only zeros? What did you hope to accomplish with the block:group >specification? > >You can always check for problems with the nonEstimable() function in >limma: > > > nonEstimable(model.matrix(~0+block+block:group)) >[1] "block1:group2" "block1:group3" "block1:group4" "block1:group5" >[5] "block2:group5" > >Best, > >Jim > > >> >> Thanks in advance for you help. >> >> Yours sincerely, >> >> Jianhong Ou >> >> LRB 710 >> Program in Gene Function and Expression >> 364 Plantation Street Worcester, >> MA 01605 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> 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 >University of Washington >Environmental and Occupational Health Sciences >4225 Roosevelt Way NE, # 100 >Seattle WA 98105-6099 >