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]]

