Question: fitting growth curve
0
gravatar for Andreia Fonseca
7.5 years ago by
Andreia Fonseca810 wrote:
Dear list, I want to fit the growth curves for cell cultures. I have three independent replicates for each cell type and I have two cell types. After I want to test if the curves are significantly different. I am trying to use grofit but I am getting the following error: TestRun <- grofit(data[1,], data[2,], TRUE) = 1. growth curve ================================= ---------------------------------------------------- Error in gcFitModel(acttime, actwell, gcID, control) : gcFitModel: length of input vectors differ! but as you can see in the data, the vectors have the same length so I don't understand... this is the data: V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 time 1 1 1 2 2.00000 2.00000 3 3 3.00000 4.00000 4.00000 4.00000 5.00000 5.0000 5.0000 cell_1 10 10 10 24 23.33333 35.00000 34 35 43.00000 81.00000 81.33333 83.33333 148.00000 115.3333 156.3333 cell_2 10 10 10 21 19.66667 21.33333 28 28 29.33333 65.33333 57.33333 63.33333 91.66667 116.3333 115.0000 session info R version 2.13.0 (2011-04-13) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] grofit_1.0 loaded via a namespace (and not attached): [1] tools_2.13.0 Thanks for the help. Kind regards, Andreia ---------------------------------------------------------------------- ------------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]
• 1.5k views
ADD COMMENTlink modified 7.5 years ago by alessandro brozzi120 • written 7.5 years ago by Andreia Fonseca810
Answer: fitting growth curve
0
gravatar for alessandro brozzi
7.5 years ago by
European Union
alessandro brozzi120 wrote:
hi Andreia, "technically" the answer is that your are not giving the right input format into the function. Look at man page about "time" and "data": ?grofit So you might try this input format for your data: time = matrix(rep(1:5,6), 6, 5, byrow=T) data = data.frame( exp_id = rep(c("cell_1", "cell_2"), c(3,3)), info=rep(c("rep1","rep2", "rep3"), 2), conc=rep(1,6) # (I set the concentration value to an arbitrary value of 1) ) tpoints = rbind( c(10, 24, 34, 81, 148), c(10.00000, 23.33333, 35.00000, 81.33333, 115.33330), c(10.00000, 35.00000 , 43.00000 , 83.33333, 156.33330), c(10.00000 ,21.00000, 28.00000, 65.33333 ,91.66667), c(10.00000, 19.66667, 28.00000, 57.33333, 116.33330), c(10.00000 , 21.33333 , 29.33333 , 63.33333 ,115.00000) ) data = cbind(data, tpoints) gcFit(time, data) should works. Then "biologically", from your description of the experimental set up, I don't think that grofit provides hypothesis tests to assess significance on the difference between two or more treatments. Unless cell_1 and cell_2 have been treated under different concentrations of a compound/drug (dose-response experimental setup). For the analysis of these data you might find good hints in the following paper "Analysis of serial measurements in medical research.": http://www.bmj.com/content/300/6719/230 or you might want to look at other packages such as: Gottardo R (2006). agce: Analysis of Growth Curve Experiments. R package version 1.2, URL http://CRAN.R-project.org/package=agce. bests, Alessandro ............................................................... *Alessandro Brozzi, PhD* Department of Mathematics and Informatics University of Perugia via Vanvitelli, 1 06123 Perugia, ITALY tel: +39 075 585 5039 mail: alessandro.brozzi@dmi.unipg.it On Wed, May 16, 2012 at 12:43 PM, Andreia Fonseca <andreia.fonseca@gmail.com> wrote: > Dear list, > > I want to fit the growth curves for cell cultures. I have three independent > replicates for each cell type and I have two cell types. After I want to > test if the curves are significantly different. I am trying to use grofit > but I am getting the following error: > > TestRun <- grofit(data[1,], data[2,], TRUE) > > = 1. growth curve ================================= > ---------------------------------------------------- > Error in gcFitModel(acttime, actwell, gcID, control) : > gcFitModel: length of input vectors differ! > > but as you can see in the data, the vectors have the same length so I don't > understand... > this is the data: > > V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 > V13 V14 V15 V16 > time 1 1 1 2 2.00000 2.00000 3 3 3.00000 4.00000 4.00000 > 4.00000 5.00000 5.0000 5.0000 > cell_1 10 10 10 24 23.33333 35.00000 34 35 43.00000 81.00000 81.33333 > 83.33333 148.00000 115.3333 156.3333 > cell_2 10 10 10 21 19.66667 21.33333 28 28 29.33333 65.33333 57.33333 > 63.33333 91.66667 116.3333 115.0000 > > session info > > R version 2.13.0 (2011-04-13) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] grofit_1.0 > > loaded via a namespace (and not attached): > [1] tools_2.13.0 > > > Thanks for the help. > Kind regards, > > Andreia > > > -------------------------------------------------------------------- --------------------------- > Andreia J. Amaral, PhD > BioFIG - Center for Biodiversity, Functional and Integrative Genomics > Instituto de Medicina Molecular > University of Lisbon > Tel: +352 217500000 (ext. office: 28253) > email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.5 years ago by alessandro brozzi120
Dear Alessandro thanks for the quick reply! :) after making the fit can I make an anova to compare the two fits? Thanks kind regards, Andreia On Wed, May 16, 2012 at 1:44 PM, alessandro brozzi < alessandro.brozzi@gmail.com> wrote: > hi Andreia, > > "technically" the answer is that your are not giving the right input > format into the function. > Look at man page about "time" and "data": > > ?grofit > > So you might try this input format for your data: > > time = matrix(rep(1:5,6), 6, 5, byrow=T) > > data = data.frame( > exp_id = rep(c("cell_1", "cell_2"), c(3,3)), > info=rep(c("rep1","rep2", "rep3"), 2), > conc=rep(1,6) # (I set the concentration value to an arbitrary value of 1) > > ) > > tpoints = rbind( > c(10, 24, 34, 81, 148), > c(10.00000, 23.33333, 35.00000, 81.33333, 115.33330), > c(10.00000, 35.00000 , 43.00000 , 83.33333, 156.33330), > c(10.00000 ,21.00000, 28.00000, 65.33333 ,91.66667), > c(10.00000, 19.66667, 28.00000, 57.33333, 116.33330), > c(10.00000 , 21.33333 , 29.33333 , 63.33333 ,115.00000) > ) > > data = cbind(data, tpoints) > > gcFit(time, data) > > should works. > > Then "biologically", from your description of the experimental set up, I > don't think that grofit provides hypothesis tests to assess significance on > the difference between two or more treatments. Unless cell_1 and cell_2 > have been treated under different concentrations of a compound/drug > (dose-response experimental setup). > > For the analysis of these data you might find good hints in the following > paper "Analysis of serial measurements in medical research.": > > http://www.bmj.com/content/300/6719/230 > > or you might want to look at other packages such as: > > Gottardo R (2006). agce: Analysis of Growth Curve Experiments. R package > version 1.2, > URL http://CRAN.R-project.org/package=agce. > > bests, > Alessandro > > ............................................................... > *Alessandro Brozzi, PhD* > Department of Mathematics and Informatics > University of Perugia > via Vanvitelli, 1 06123 Perugia, ITALY > tel: +39 075 585 5039 > mail: alessandro.brozzi@dmi.unipg.it > > > On Wed, May 16, 2012 at 12:43 PM, Andreia Fonseca < > andreia.fonseca@gmail.com> wrote: > >> Dear list, >> >> I want to fit the growth curves for cell cultures. I have three >> independent >> replicates for each cell type and I have two cell types. After I want to >> test if the curves are significantly different. I am trying to use grofit >> but I am getting the following error: >> >> TestRun <- grofit(data[1,], data[2,], TRUE) >> >> = 1. growth curve ================================= >> ---------------------------------------------------- >> Error in gcFitModel(acttime, actwell, gcID, control) : >> gcFitModel: length of input vectors differ! >> >> but as you can see in the data, the vectors have the same length so I >> don't >> understand... >> this is the data: >> >> V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 >> V13 V14 V15 V16 >> time 1 1 1 2 2.00000 2.00000 3 3 3.00000 4.00000 4.00000 >> 4.00000 5.00000 5.0000 5.0000 >> cell_1 10 10 10 24 23.33333 35.00000 34 35 43.00000 81.00000 81.33333 >> 83.33333 148.00000 115.3333 156.3333 >> cell_2 10 10 10 21 19.66667 21.33333 28 28 29.33333 65.33333 57.33333 >> 63.33333 91.66667 116.3333 115.0000 >> >> session info >> >> R version 2.13.0 (2011-04-13) >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] grofit_1.0 >> >> loaded via a namespace (and not attached): >> [1] tools_2.13.0 >> >> >> Thanks for the help. >> Kind regards, >> >> Andreia >> >> >> ------------------------------------------------------------------- ---------------------------- >> Andreia J. Amaral, PhD >> BioFIG - Center for Biodiversity, Functional and Integrative Genomics >> Instituto de Medicina Molecular >> University of Lisbon >> Tel: +352 217500000 (ext. office: 28253) >> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- ---------------------------------------------------------------------- ----------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]
ADD REPLYlink written 7.5 years ago by Andreia Fonseca810
yes, you might also make an ANOVA on the slopes (in case of two only different cell lines it's the same of performing a t-test) On Wed, May 16, 2012 at 2:53 PM, Andreia Fonseca <andreia.fonseca@gmail.com>wrote: > Dear Alessandro thanks for the quick reply! :) > > after making the fit can I make an anova to compare the two fits? > > Thanks > > kind regards, > > Andreia > > > > On Wed, May 16, 2012 at 1:44 PM, alessandro brozzi < > alessandro.brozzi@gmail.com> wrote: > >> hi Andreia, >> >> "technically" the answer is that your are not giving the right input >> format into the function. >> Look at man page about "time" and "data": >> >> ?grofit >> >> So you might try this input format for your data: >> >> time = matrix(rep(1:5,6), 6, 5, byrow=T) >> >> data = data.frame( >> exp_id = rep(c("cell_1", "cell_2"), c(3,3)), >> info=rep(c("rep1","rep2", "rep3"), 2), >> conc=rep(1,6) # (I set the concentration value to an arbitrary value of >> 1) >> >> ) >> >> tpoints = rbind( >> c(10, 24, 34, 81, 148), >> c(10.00000, 23.33333, 35.00000, 81.33333, 115.33330), >> c(10.00000, 35.00000 , 43.00000 , 83.33333, 156.33330), >> c(10.00000 ,21.00000, 28.00000, 65.33333 ,91.66667), >> c(10.00000, 19.66667, 28.00000, 57.33333, 116.33330), >> c(10.00000 , 21.33333 , 29.33333 , 63.33333 ,115.00000) >> ) >> >> data = cbind(data, tpoints) >> >> gcFit(time, data) >> >> should works. >> >> Then "biologically", from your description of the experimental set up, I >> don't think that grofit provides hypothesis tests to assess significance on >> the difference between two or more treatments. Unless cell_1 and cell_2 >> have been treated under different concentrations of a compound/drug >> (dose-response experimental setup). >> >> For the analysis of these data you might find good hints in the following >> paper "Analysis of serial measurements in medical research.": >> >> http://www.bmj.com/content/300/6719/230 >> >> or you might want to look at other packages such as: >> >> Gottardo R (2006). agce: Analysis of Growth Curve Experiments. R package >> version 1.2, >> URL http://CRAN.R-project.org/package=agce. >> >> bests, >> Alessandro >> >> ............................................................... >> *Alessandro Brozzi, PhD* >> Department of Mathematics and Informatics >> University of Perugia >> via Vanvitelli, 1 06123 Perugia, ITALY >> tel: +39 075 585 5039 >> mail: alessandro.brozzi@dmi.unipg.it >> >> >> On Wed, May 16, 2012 at 12:43 PM, Andreia Fonseca < >> andreia.fonseca@gmail.com> wrote: >> >>> Dear list, >>> >>> I want to fit the growth curves for cell cultures. I have three >>> independent >>> replicates for each cell type and I have two cell types. After I want to >>> test if the curves are significantly different. I am trying to use grofit >>> but I am getting the following error: >>> >>> TestRun <- grofit(data[1,], data[2,], TRUE) >>> >>> = 1. growth curve ================================= >>> ---------------------------------------------------- >>> Error in gcFitModel(acttime, actwell, gcID, control) : >>> gcFitModel: length of input vectors differ! >>> >>> but as you can see in the data, the vectors have the same length so I >>> don't >>> understand... >>> this is the data: >>> >>> V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 >>> V13 V14 V15 V16 >>> time 1 1 1 2 2.00000 2.00000 3 3 3.00000 4.00000 4.00000 >>> 4.00000 5.00000 5.0000 5.0000 >>> cell_1 10 10 10 24 23.33333 35.00000 34 35 43.00000 81.00000 81.33333 >>> 83.33333 148.00000 115.3333 156.3333 >>> cell_2 10 10 10 21 19.66667 21.33333 28 28 29.33333 65.33333 57.33333 >>> 63.33333 91.66667 116.3333 115.0000 >>> >>> session info >>> >>> R version 2.13.0 (2011-04-13) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] grofit_1.0 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.13.0 >>> >>> >>> Thanks for the help. >>> Kind regards, >>> >>> Andreia >>> >>> >>> ------------------------------------------------------------------ ----------------------------- >>> Andreia J. Amaral, PhD >>> BioFIG - Center for Biodiversity, Functional and Integrative Genomics >>> Instituto de Medicina Molecular >>> University of Lisbon >>> Tel: +352 217500000 (ext. office: 28253) >>> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > > > -- > > -------------------------------------------------------------------- ------------------------- > Andreia J. Amaral, PhD > BioFIG - Center for Biodiversity, Functional and Integrative Genomics > Instituto de Medicina Molecular > University of Lisbon > Tel: +352 217500000 (ext. office: 28253) > email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt > > [[alternative HTML version deleted]]
ADD REPLYlink written 7.5 years ago by alessandro brozzi120
Dear Alessandro, I have tried your code and it works but it is making a fit for each replicate. I aim to make a fit for each cell type. Is this possible with your package? Kind regards, Andreia On Wed, May 16, 2012 at 2:24 PM, alessandro brozzi < alessandro.brozzi@gmail.com> wrote: > yes, > you might also make an ANOVA on the slopes (in case of two only different > cell lines it's the same of performing a t-test) > > > On Wed, May 16, 2012 at 2:53 PM, Andreia Fonseca < > andreia.fonseca@gmail.com> wrote: > >> Dear Alessandro thanks for the quick reply! :) >> >> after making the fit can I make an anova to compare the two fits? >> >> Thanks >> >> kind regards, >> >> Andreia >> >> >> >> On Wed, May 16, 2012 at 1:44 PM, alessandro brozzi < >> alessandro.brozzi@gmail.com> wrote: >> >>> hi Andreia, >>> >>> "technically" the answer is that your are not giving the right input >>> format into the function. >>> Look at man page about "time" and "data": >>> >>> ?grofit >>> >>> So you might try this input format for your data: >>> >>> time = matrix(rep(1:5,6), 6, 5, byrow=T) >>> >>> data = data.frame( >>> exp_id = rep(c("cell_1", "cell_2"), c(3,3)), >>> info=rep(c("rep1","rep2", "rep3"), 2), >>> conc=rep(1,6) # (I set the concentration value to an arbitrary value of >>> 1) >>> >>> ) >>> >>> tpoints = rbind( >>> c(10, 24, 34, 81, 148), >>> c(10.00000, 23.33333, 35.00000, 81.33333, 115.33330), >>> c(10.00000, 35.00000 , 43.00000 , 83.33333, 156.33330), >>> c(10.00000 ,21.00000, 28.00000, 65.33333 ,91.66667), >>> c(10.00000, 19.66667, 28.00000, 57.33333, 116.33330), >>> c(10.00000 , 21.33333 , 29.33333 , 63.33333 ,115.00000) >>> ) >>> >>> data = cbind(data, tpoints) >>> >>> gcFit(time, data) >>> >>> should works. >>> >>> Then "biologically", from your description of the experimental set up, I >>> don't think that grofit provides hypothesis tests to assess significance on >>> the difference between two or more treatments. Unless cell_1 and cell_2 >>> have been treated under different concentrations of a compound/drug >>> (dose-response experimental setup). >>> >>> For the analysis of these data you might find good hints in the >>> following paper "Analysis of serial measurements in medical research.": >>> >>> http://www.bmj.com/content/300/6719/230 >>> >>> or you might want to look at other packages such as: >>> >>> Gottardo R (2006). agce: Analysis of Growth Curve Experiments. R package >>> version 1.2, >>> URL http://CRAN.R-project.org/package=agce. >>> >>> bests, >>> Alessandro >>> >>> ............................................................... >>> *Alessandro Brozzi, PhD* >>> Department of Mathematics and Informatics >>> University of Perugia >>> via Vanvitelli, 1 06123 Perugia, ITALY >>> tel: +39 075 585 5039 >>> mail: alessandro.brozzi@dmi.unipg.it >>> >>> >>> On Wed, May 16, 2012 at 12:43 PM, Andreia Fonseca < >>> andreia.fonseca@gmail.com> wrote: >>> >>>> Dear list, >>>> >>>> I want to fit the growth curves for cell cultures. I have three >>>> independent >>>> replicates for each cell type and I have two cell types. After I want to >>>> test if the curves are significantly different. I am trying to use >>>> grofit >>>> but I am getting the following error: >>>> >>>> TestRun <- grofit(data[1,], data[2,], TRUE) >>>> >>>> = 1. growth curve ================================= >>>> ---------------------------------------------------- >>>> Error in gcFitModel(acttime, actwell, gcID, control) : >>>> gcFitModel: length of input vectors differ! >>>> >>>> but as you can see in the data, the vectors have the same length so I >>>> don't >>>> understand... >>>> this is the data: >>>> >>>> V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 >>>> V13 V14 V15 V16 >>>> time 1 1 1 2 2.00000 2.00000 3 3 3.00000 4.00000 >>>> 4.00000 >>>> 4.00000 5.00000 5.0000 5.0000 >>>> cell_1 10 10 10 24 23.33333 35.00000 34 35 43.00000 81.00000 81.33333 >>>> 83.33333 148.00000 115.3333 156.3333 >>>> cell_2 10 10 10 21 19.66667 21.33333 28 28 29.33333 65.33333 57.33333 >>>> 63.33333 91.66667 116.3333 115.0000 >>>> >>>> session info >>>> >>>> R version 2.13.0 (2011-04-13) >>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] grofit_1.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tools_2.13.0 >>>> >>>> >>>> Thanks for the help. >>>> Kind regards, >>>> >>>> Andreia >>>> >>>> >>>> ----------------------------------------------------------------- ------------------------------ >>>> Andreia J. Amaral, PhD >>>> BioFIG - Center for Biodiversity, Functional and Integrative Genomics >>>> Instituto de Medicina Molecular >>>> University of Lisbon >>>> Tel: +352 217500000 (ext. office: 28253) >>>> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> >> >> -- >> >> ------------------------------------------------------------------- -------------------------- >> Andreia J. Amaral, PhD >> BioFIG - Center for Biodiversity, Functional and Integrative Genomics >> Instituto de Medicina Molecular >> University of Lisbon >> Tel: +352 217500000 (ext. office: 28253) >> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt >> >> > -- ---------------------------------------------------------------------- ----------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]
ADD REPLYlink written 7.5 years ago by Andreia Fonseca810
hi Andreia, On Thu, May 17, 2012 at 2:43 PM, Andreia Fonseca <andreia.fonseca@gmail.com>wrote: > Dear Alessandro, > > I have tried your code and it works but it is making a fit for each > replicate. I aim to make a fit for each cell type. what you might want to do is to fit a model for each single curve and consider a characteristic parameter, for instance the maximum slope \mu. Then you might test to detect significant difference between the \mu estimated in different conditions (cell type). It is also mentioned in the vignettes of the package: "[...]For example, if growth curves for a control and a treatment situation are to be compared one can use a two sample statistical test to detect significant effects of the treatment.[...]" > Is this possible with your package? > I am not the author of this package. Info about "grofit" package are available at: http://cran.r-project.org/web/packages/grofit/index.html cheers, Alex > > Kind regards, > > Andreia > > > On Wed, May 16, 2012 at 2:24 PM, alessandro brozzi < > alessandro.brozzi@gmail.com> wrote: > >> yes, >> you might also make an ANOVA on the slopes (in case of two only different >> cell lines it's the same of performing a t-test) >> >> >> On Wed, May 16, 2012 at 2:53 PM, Andreia Fonseca < >> andreia.fonseca@gmail.com> wrote: >> >>> Dear Alessandro thanks for the quick reply! :) >>> >>> after making the fit can I make an anova to compare the two fits? >>> >>> Thanks >>> >>> kind regards, >>> >>> Andreia >>> >>> >>> >>> On Wed, May 16, 2012 at 1:44 PM, alessandro brozzi < >>> alessandro.brozzi@gmail.com> wrote: >>> >>>> hi Andreia, >>>> >>>> "technically" the answer is that your are not giving the right input >>>> format into the function. >>>> Look at man page about "time" and "data": >>>> >>>> ?grofit >>>> >>>> So you might try this input format for your data: >>>> >>>> time = matrix(rep(1:5,6), 6, 5, byrow=T) >>>> >>>> data = data.frame( >>>> exp_id = rep(c("cell_1", "cell_2"), c(3,3)), >>>> info=rep(c("rep1","rep2", "rep3"), 2), >>>> conc=rep(1,6) # (I set the concentration value to an arbitrary value >>>> of 1) >>>> >>>> ) >>>> >>>> tpoints = rbind( >>>> c(10, 24, 34, 81, 148), >>>> c(10.00000, 23.33333, 35.00000, 81.33333, 115.33330), >>>> c(10.00000, 35.00000 , 43.00000 , 83.33333, 156.33330), >>>> c(10.00000 ,21.00000, 28.00000, 65.33333 ,91.66667), >>>> c(10.00000, 19.66667, 28.00000, 57.33333, 116.33330), >>>> c(10.00000 , 21.33333 , 29.33333 , 63.33333 ,115.00000) >>>> ) >>>> >>>> data = cbind(data, tpoints) >>>> >>>> gcFit(time, data) >>>> >>>> should works. >>>> >>>> Then "biologically", from your description of the experimental set up, >>>> I don't think that grofit provides hypothesis tests to assess significance >>>> on the difference between two or more treatments. Unless cell_1 and cell_2 >>>> have been treated under different concentrations of a compound/drug >>>> (dose-response experimental setup). >>>> >>>> For the analysis of these data you might find good hints in the >>>> following paper "Analysis of serial measurements in medical research.": >>>> >>>> http://www.bmj.com/content/300/6719/230 >>>> >>>> or you might want to look at other packages such as: >>>> >>>> Gottardo R (2006). agce: Analysis of Growth Curve Experiments. R >>>> package version 1.2, >>>> URL http://CRAN.R-project.org/package=agce. >>>> >>>> bests, >>>> Alessandro >>>> >>>> ............................................................... >>>> *Alessandro Brozzi, PhD* >>>> Department of Mathematics and Informatics >>>> University of Perugia >>>> via Vanvitelli, 1 06123 Perugia, ITALY >>>> tel: +39 075 585 5039 >>>> mail: alessandro.brozzi@dmi.unipg.it >>>> >>>> >>>> On Wed, May 16, 2012 at 12:43 PM, Andreia Fonseca < >>>> andreia.fonseca@gmail.com> wrote: >>>> >>>>> Dear list, >>>>> >>>>> I want to fit the growth curves for cell cultures. I have three >>>>> independent >>>>> replicates for each cell type and I have two cell types. After I want >>>>> to >>>>> test if the curves are significantly different. I am trying to use >>>>> grofit >>>>> but I am getting the following error: >>>>> >>>>> TestRun <- grofit(data[1,], data[2,], TRUE) >>>>> >>>>> = 1. growth curve ================================= >>>>> ---------------------------------------------------- >>>>> Error in gcFitModel(acttime, actwell, gcID, control) : >>>>> gcFitModel: length of input vectors differ! >>>>> >>>>> but as you can see in the data, the vectors have the same length so I >>>>> don't >>>>> understand... >>>>> this is the data: >>>>> >>>>> V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 >>>>> V13 V14 V15 V16 >>>>> time 1 1 1 2 2.00000 2.00000 3 3 3.00000 4.00000 >>>>> 4.00000 >>>>> 4.00000 5.00000 5.0000 5.0000 >>>>> cell_1 10 10 10 24 23.33333 35.00000 34 35 43.00000 81.00000 81.33333 >>>>> 83.33333 148.00000 115.3333 156.3333 >>>>> cell_2 10 10 10 21 19.66667 21.33333 28 28 29.33333 65.33333 57.33333 >>>>> 63.33333 91.66667 116.3333 115.0000 >>>>> >>>>> session info >>>>> >>>>> R version 2.13.0 (2011-04-13) >>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>>> >>>>> locale: >>>>> [1] C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] grofit_1.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.13.0 >>>>> >>>>> >>>>> Thanks for the help. >>>>> Kind regards, >>>>> >>>>> Andreia >>>>> >>>>> >>>>> ---------------------------------------------------------------- ------------------------------- >>>>> Andreia J. Amaral, PhD >>>>> BioFIG - Center for Biodiversity, Functional and Integrative Genomics >>>>> Instituto de Medicina Molecular >>>>> University of Lisbon >>>>> Tel: +352 217500000 (ext. office: 28253) >>>>> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>>> >>> >>> >>> -- >>> >>> ------------------------------------------------------------------ --------------------------- >>> Andreia J. Amaral, PhD >>> BioFIG - Center for Biodiversity, Functional and Integrative Genomics >>> Instituto de Medicina Molecular >>> University of Lisbon >>> Tel: +352 217500000 (ext. office: 28253) >>> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt >>> >>> >> > > > -- > > -------------------------------------------------------------------- ------------------------- > Andreia J. Amaral, PhD > BioFIG - Center for Biodiversity, Functional and Integrative Genomics > Instituto de Medicina Molecular > University of Lisbon > Tel: +352 217500000 (ext. office: 28253) > email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt > > [[alternative HTML version deleted]]
ADD REPLYlink written 7.5 years ago by alessandro brozzi120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 374 users visited in the last hour