Hi Thanks a lot, I think you have covered the things I want to do for now so I will try to implement them as soon I can.
<< A finite Fourier series could be the best tool IF the the multiple periodicities are all integer fractions of a common scale.>> This is certainly true for my repetitive "unit" (the smallest data peak) so I hope this makes things easier. Thanks spencerg wrote: > > Dear Dr Gkikopoulos: > > > 1. Have you looked at "bioconductor.org"? They have substantive > extensions to R specifically for "genomic data", which I assume would > include chromosome. > > > 2. To "identify periodicities at different timescales", I agree > with Stephen that "spectrum" would likely help. > > > 3. The best software to "fit data into discrete number of curves" > depends on the particular "discrete number of curves" you want to > consider and how you want to "fit data into" them. A finite Fourier > series could be the best tool IF the the multiple periodicities are all > integer fractions of a common scale. In that case, using a "fourier" > base in the "fda" package could be your method of choice. Otherwise, > you might consider Bayesian Model Averaging. RSiteSearch("Bayesian > Model Averaging") produced 80 hits for me just now, and > RSiteSearch("Bayesian Model Averaging", "function") produced 60. > "RSiteSearch.function" in the "RSiteSearch" package [available via > install.packages("RSiteSearch",repos="http://r-forge.r-project.org")] > told me that 27 of the 60 were in the "ensembleBMA" package, and another > 14 were in the "BMA" package. > > > 4. The best way to "compare data from different experiments" > depends on your evaluation of "3" above. The "fda" package includes an > "fRegress" function that might be useful. > > > Hope this helps. > Spencer Graves > > > trias wrote: >> There are a couple of different goals for this projects >> >> *identify periodicities at different timescales (ie different dT) >> *fit data into discrete number of curves, ie 6 different basic functions >> should be enough to describe the basic repeating elements in this data >> (ie 6 >> different categories of peaks) >> *comapre data from different experiments of the same "time" reference >> (in >> my case this is location on chromosome) for changes in the underlying >> basic >> elements (ie changes of the basic funtions,periodicity etc) >> >> I think if I can find a strategy to answer some of these question I be >> in a >> good position to explore this data analysis further if needed. >> >> Thanks a lot >> >> >> >> stephen sefick wrote: >> >>> What is your end goal? If it is to try and account for the >>> variability of the "timeseries" you may want to look at ?spectrum >>> If it is to model the periodicity... >>> >>> Stephen Sefick >>> >>> On Fri, Apr 3, 2009 at 11:30 AM, trias <t.gkikopou...@dundee.ac.uk> >>> wrote: >>> >>>> Here is the gif that didn't come through earlier >>>> http://www.nabble.com/file/p22870832/signal.gif signal.gif >>>> -- >>>> View this message in context: >>>> http://www.nabble.com/Curve-fitting%2CFDA-for-biological-data-tp22868069p22870832.html >>>> Sent from the R help mailing list archive at Nabble.com. >>>> >>>> ______________________________________________ >>>> R-help@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide >>>> http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>>> >>> >>> -- >>> Stephen Sefick >>> >>> Let's not spend our time and resources thinking about things that are >>> so little or so large that all they really do for us is puff us up and >>> make us feel like gods. We are mammals, and have not exhausted the >>> annoying little problems of being mammals. >>> >>> -K. Mullis >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >>> >>> >> >> > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/Curve-fitting%2CFDA-for-biological-data-tp22868069p23024818.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.