Or alternatively use the standard R-functions lm or lm.fit for performing a linear regression in R. (x is the design matrix and y is the transpose of the matrix containing the signals.) Holger -------- Original-Nachricht -------- > Datum: Fri, 30 Jan 2009 09:18:15 -0600 > Von: Jenny Drnevich <drnevich at="" illinois.edu=""> > An: Daniel Brewer <daniel.brewer at="" icr.ac.uk="">, Bioconductor mailing list <bioconductor at="" stat.math.ethz.ch=""> > Betreff: Re: [BioC] Limma without eBayes correction > Hi Daniel, > > I have had to do this occasionally. See section 10.2, Fitted Model > Objects. It shows how to get the ordinary t-stats from the fit object > after calling just lmFit(). This is how ebayes calculates the > p-values, so just substitute in the ordinary t-values and fit$df.residual: > > out$p.value <- 2 * pt(-abs(out$t), df = df.total) > > Cheers, > Jenny > > At 09:02 AM 1/30/2009, Daniel Brewer wrote: > >Hi, > > > >I normally use the eBayes correction and I am very happy about it, but I > >am trying to check some analysis performed by someone else and they used > >straight linear models with no correction. I am no its not recommended, > >but its the situation I have to deal with. > > > >How do I use limma without eBayes? I read somewhere that it is in the > >Limma's user guide but I can't for the life of me find it. > > > >Thanks > > > >Dan > > > >-- > >************************************************************** > >Daniel Brewer, Ph.D. > > > >Institute of Cancer Research > >Molecular Carcinogenesis > >Email: daniel.brewer at icr.ac.uk > >************************************************************** > > > >The Institute of Cancer Research: Royal Cancer Hospital, a > >charitable Company Limited by Guarantee, Registered in England under > >Company No. 534147 with its Registered Office at 123 Old Brompton > >Road, London SW7 3RP. > > > >This e-mail message is confidential and for use by the a...{{dropped:2}} > > > >_______________________________________________ > >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 > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > _______________________________________________ > 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 --