limma user's guide example

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Giovanni Coppola ▴ 250

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ADD COMMENT • link updated 18.2 years ago by Naomi Altman ★ 6.0k • written 18.2 years ago by Giovanni Coppola ▴ 250

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James W. MacDonald 67k

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Hi Giovanni, Giovanni Coppola wrote: > Sorry guys, another DQ (dumb question).... > Limma User's Guide pag. 39 and 42, line: > cont.matrix <- makeContrasts(MUvsWT=WT-MU, levels=design) > Why not MU-WT? It doesn't matter, really. I generally do what you suggest because then a positive log difference indicates up-regulation in mutant and negative indicates down-regulation. This seems to be more intuitive for my Biologist friends. However, other than the sign of the statistic, there is no difference. Best, Jim > Thanks > Giovanni > > > > [[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 -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD COMMENT • link 18.2 years ago James W. MacDonald 67k

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Naomi Altman ★ 6.0k

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You can do it either way and you will obtain the same p-values. Of course, the sign of M will be reversed. --Naomi At 03:58 PM 10/4/2006, Giovanni Coppola wrote: >Sorry guys, another DQ (dumb question).... >Limma User's Guide pag. 39 and 42, line: >cont.matrix <- makeContrasts(MUvsWT=WT-MU, levels=design) >Why not MU-WT? >Thanks >Giovanni > > > > [[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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

ADD COMMENT • link 18.2 years ago Naomi Altman ★ 6.0k

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Hi Naomi and Jim, thanks for your replies. I agree that genes and p-values will stay the same. However, for this particular example, two possible approaches are presented, and - as they stand now - they are conflicting, yielding results with opposite signs. Best Giovanni On Oct 4, 2006, at 1:19 PM, Naomi Altman wrote: > You can do it either way and you will obtain the same p-values. Of > course, the sign of M will be reversed. > > > --Naomi > > At 03:58 PM 10/4/2006, Giovanni Coppola wrote: >> Sorry guys, another DQ (dumb question).... >> Limma User's Guide pag. 39 and 42, line: >> cont.matrix <- makeContrasts(MUvsWT=WT-MU, levels=design) >> Why not MU-WT? >> Thanks >> Giovanni >> >> >> >> [[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 > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 > (Statistics) > University Park, PA 16802-2111 >

ADD REPLY • link 18.2 years ago Giovanni Coppola ▴ 250

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