design matrix with limma
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Diya v ▴ 20
@diya-v-3664
Last seen 9.5 years ago

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

limma • 1.8k views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States
-- 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
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