Limma -time course - no replicates
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Lana Schaffer ★ 1.3k
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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
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Naomi Altman ★ 6.0k
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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
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Naomi, Can you please suggest a routine or software for us to use? Lana ________________________________________ From: Naomi Altman [naomi@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
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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
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Naomi Altman ★ 6.0k
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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
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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
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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
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Naomi Altman ★ 6.0k
@naomi-altman-380
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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
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