limma user's guide example
2
0
Entering edit mode
@giovanni-coppola-893
Last seen 9.6 years ago
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061004/ 16c10f26/attachment.pl
• 757 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 14 hours ago
United States
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
0
Entering edit mode
Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 2.9 years ago
United States
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
0
Entering edit mode
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

Login before adding your answer.

Traffic: 704 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6