Question: design matrix with limma
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gravatar for Diya v
10.1 years ago by
Diya v20
Diya v20 wrote:
Hi, I have a question.I have 2control samples(v7,v8) and 2 treatment samples(g1,g4).I have the data generated from aroma.affymetrix and I have applied log2 on it and load the data for doing statistical analysis by limma.Is my design matrix correct? dat.m<-read.csv("datam.csv",skip=0) genes<-rownames(dat.m) groups<-c(C,C,T,T) groups<-as.factor(groups) design<-model.matrix(~groups) design fit<-lmFit(dat.m, design) fit<-eBayes(fit) toptable(fit, coef=2) Thanks, Diya Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com [[alternative HTML version deleted]]
limma • 1.4k views
ADD COMMENTlink modified 4 weeks ago by kobayotay0 • written 10.1 years ago by Diya v20
Answer: design matrix with limma
1
gravatar for James W. MacDonald
10.1 years ago by
United States
James W. MacDonald51k wrote:
-- 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 >>> Diya v <diya_2208 at="" yahoo.co.in=""> wrote: > Hi, > > I have a question.I have 2control samples(v7,v8) and 2 treatment > samples(g1,g4).I have the data generated from aroma.affymetrix and I > have applied log2 on it and load the data for doing statistical > analysis by limma.Is my design matrix correct? Yes. Best, Jim > > dat.m<-read.csv("datam.csv",skip=0) > genes<-rownames(dat.m) > groups<-c(C,C,T,T) > groups<-as.factor(groups) > design<-model.matrix(~groups) > design > fit<-lmFit(dat.m, design) > fit<-eBayes(fit) > toptable(fit, coef=2) > > Thanks, > Diya > > > > Love Cricket? Check out live scores, photos, video highlights and > more. Click here http://cricket.yahoo.com > [[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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 10.1 years ago by James W. MacDonald51k

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ADD REPLYlink written 7 days ago by farahhtan120
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