Hi, On Sun, Jun 6, 2010 at 2:11 AM, Lana Schaffer <schaffer at="" scripps.edu=""> wrote: > Naomi, > Can you please suggest a routine or software for us to use? If you go to the bioconductor page: http://www.bioconductor.org/packages/release/bioc/ and search that page for the word "time", you'll find several packages relating to "time course" or "time series". Perhaps those could be helpful? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Hi, Lana: I have the similar question without biological replicates, and not yet confirmed. I am aware of my experiment was not well set-up strictly following to MIAME, which is quite common in plant research. This is my experiment is: >> FileName DPA Cy3 Cy5 >> 2009-07-10-atq3.7.3.145-15.gpr 15DPA WT MUTANT >> 2009-07-15-atq3.7.3.146-15.gpr 15DPA MUTANT WT >> 2009-07-15-atq3.7.3.147-15.gpr 15DPA MUTANT WT >> 2009-07-15-atq3.7.3.148-15.gpr 15DPA WT MUTANT >> 2009-07-15-atq3.7.3.149-15.gpr 15DPA WT MUTANT >> 2009-07-17-atq3.7.3.151-20.gpr 20DPA MUTANT WT >> 2009-07-17-atq3.7.3.152-20.gpr 20DPA WT MUTANT >> 2009-07-17-atq3.7.3.153-25.gpr 25DPA MUTANT WT >> 2009-07-17-atq3.7.3.154-25.gpr 25DPA WT MUTANT >> 2009-07-17-atq3.7.3.155-10.gpr 10DPA MUTANT WT >> 2009-07-17-atq3.7.3.156-10.gpr 10DPA WT MUTANT >> 2009-07-17-atq3.7.3.157-30.gpr 30DPA MUTANT WT >> 2009-07-17-atq3.7.3.158-30.gpr 30DPA WT MUTANT >> 2009-07-21-atq3.7.3-159-10.gpr 10DPA MUTANT WT >> 2009-07-21-atq3.7.3-160-20.gpr 20DPA MUTANT WT >> 2009-07-21-atq3.7.3-164-25.gpr 25DPA MUTANT WT >> 2009-07-21-atq3.7.3-256-30.gpr 30DPA MUTANT WT >> 2009-07-22-atq3.7.3-115-10.gpr 10DPA MUTANT WT >> 2009-07-22-atq3.7.3-116-20.gpr 20DPA MUTANT WT >> 2009-07-22-atq3.7.3-117-25.gpr 25DPA MUTANT WT >> 2009-07-22-atq3.7.3-118-30.gpr 30DPA MUTANT WT >> 2009-07-22-atq3.7.3-119-10.gpr 10DPA WT MUTANT >> 2009-07-22-atq3.7.3-120-20.gpr 20DPA WT MUTANT >> 2009-07-22-atq3.7.3-124-25.gpr 25DPA WT MUTANT >> 2009-07-22-atq3.7.3-125-30.gpr 30DPA WT MUTANT Thanks any one, especially Naomi, who can give some suggestions. Yifang -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Lana Schaffer Sent: Tuesday, June 08, 2010 10:29 AM To: Naomi Altman; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Limma -time course - no replicates Naomi, Thanks. Can you give an example how to set up the design matrix? Lana ________________________________________ From: Naomi Altman [naomi@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 _______________________________________________ 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