
Dear James,
Thank you very much for your reply!
 
For my question:
> Which genes have estrogen effect (up/down between absent and present) > CONSISTENTLY at both 10 hours and 48 hours?> 
 I am more interested in whether I can  add one contrast in either design or contrast matrix to dothis job ???
 
Is it the one way to look the intersection of the two comparisons for answering the question?
 
Qin Kuang
 
 
 
 
> Date: Tue, 22 Jan 2008 09:18:31 -0500> From: jmacdon@med.umich.edu> To: kuang_qin@hotmail.com> CC: bioconductor@stat.math.ethz.ch> Subject: Re: [BioC] Limma -Time series data> > kuangqin wrote:> > > > > > Dear Helper> > > > > > For the Estrogen data given in limma usersguide, we can estimate estrogen effect and > > the time-estrogen interaction as follows> > > >> design=matrix(c(1,1,1,1,1,1,1,1,> > + 0,0,0,0,1,1,1,1,> > + 0,0,1,1,0,0,0,0,> > + 0,0,0,0,0,0,1,1),nrow=8,ncol=4, byrow=F)> >> rownames(design)= treatments> >> colnames(design)= c("Intercept","Time","E10","E48")> >>> >> design> > Intercept Time E10 E48> > e10 1 0 0 0> > e10 1 0 0 0> > E10 1 0 1 0> > E10 1 0 1 0> > e48 1 1 0 0> > e48 1 1 0 0> > E48 1 1 0 1> > E48 1 1 0 1> >> cont.matrix <- cbind(E10=c(0,0,1,0),E48=c(0,0,0,1),"E48-E10"=c(0,0,1,-1) )> >> cont.matrix> > E10 E48 E48-E10> > [1,] 0 0 0> > [2,] 0 0 0> > [3,] 1 0 1> > [4,] 0 1 -1> > > > The first and second coefficients (in cont.matrix) estimate the estrogen effect > > at 10 hours and 48 hours ,respectively. The third coefficient (in cont.matrix) > > estimates the time-estrogen interaction.> > > > Here I want to ask another question:> > > > Which genes have estrogen effect (up/down between absent and present) > > CONSISTENTLY at both 10 hours and 48 hours?> > > > I am not sure how to add one item in either design or contrast matrix to do> > this job ???> > > > Is it an efficient way to just simply look the intersection of genes selected in > > first and second coefficients (in cont.matrix)?> > I think you want ?decideTests and ?vennDiagram. The decideTests() > function will output a matrix that you can use to identify the genes > that are up or down regulated in the intersection of the two comparisons.> > Best,> > Jim> > > > > > Thank you very much for your help in advance !!!> > > > Qin Kuang> > > > > > > > > > > > > > > > > > > > > > > > _________________________________________________________________> > ÌìÁ¹ÁË£¬ÌíÒÂÁË£¬ÐÄ¶¯ÁË£¬¡°Æß¼þ¡±ÁË > > http://get.live.cn> > [[alternative HTML version deleted]]> > > > > > > > ------------------------------------------------------------------------> > > > _______________________________________________> > Bioconductor mailing list> > Bioconductor@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> Affymetrix and cDNA Microarray Core> University of Michigan Cancer Center> 1500 E. Medical Center Drive> 7410 CCGC> Ann Arbor MI 48109> 734-647-5623
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