Hi Naomi, Thank you for pointing out this example, its really useful. Can you explain the meaning of the p.value and F.p.value in this case? Which one should be used? time=1:10 design=model.matrix(~time) fit=eBayes(lmFit(data, design)) Thank you. Yair on 6/8/10 3:53 PM, Naomi Altman at naomi at stat.psu.edu wrote: > time=1:10 > design=model.matrix(~time) > > > > At 12:28 PM 6/8/2010, Lana Schaffer wrote: >> Naomi, >> Thanks. >> Can you give an example how to set up the design matrix? >> Lana >> >> ________________________________________ >> From: Naomi Altman [naomi at stat.psu.edu] >> Sent: Tuesday, June 08, 2010 7:49 AM >> To: Lana Schaffer; Naomi Altman; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Limma -time course - no replicates >> >> You can use LIMMA. The key is to have time be a continuous variable, >> not a factor. So time (or a function of time) is entered into the >> design matrix, instead of +/- 1 or 0. >> >> --Naomi >> >> At 02:11 AM 6/6/2010, Lana Schaffer wrote: >>> Naomi, >>> Can you please suggest a routine or software for us to use? >>> Lana >>> >>> ________________________________________ >>> From: Naomi Altman [naomi at stat.psu.edu] >>> Sent: Friday, June 04, 2010 6:49 PM >>> To: Lana Schaffer; bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] Limma -time course - no replicates >>> >>> Only if you consider this to be a regression on a function of time, >>> instead of an ANOVA. >>> >>> --naomi >>> >>> At 07:12 PM 6/4/2010, Lana Schaffer wrote: >>>> Hi, >>>> We are trying to use Limma code for a Time Course Experiment without >>>> Replicates for 4 times. From looking at the manual, looks like don't >>>> Need replicates. But the ebayes routine complains about no residual >>>> Degrees of freedom. >>>> Can we use Limma for Time Course without replicates? >>>> Lana >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 > > 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 > > _______________________________________________ > 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