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
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