Limma without eBayes correction
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Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 10.3 years ago
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}}
Cancer limma Cancer limma • 1.2k views
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 10 days ago
United States
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
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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 --
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@james-w-macdonald-5106
Last seen 6 days ago
United States
Hi Dan, p. 54 Best, Jim 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 > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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