[R] Support vector model?

Celine Carret ckc at sanger.ac.uk
Fri Dec 12 12:10:12 CET 2008

Dear All,

Apologies for sending this email to both list, but at this point I'm not
sure which one could help me the most.

I have 4 sets of data, 1 test and 3 different sets of controls.
The measurements are binary, with a matrix of 0 and 1
I'm measuring across time (rows, ~815) the behaviour of organelles in
the cell by microscopy in response to different stimuli (several
measurements for each set, 57 columns in total)
Set 1: parasite test
Set 2: no stimulus
Set 3: inert stimulus (beads)
Set 4: different pathogen
Across time, a "zero" means nothing happens around my parasite
introduced in the cell, a "1" means some cytoskeleton dynamics occurring
around my parasite
I want to give some statistical value to my observations in saying that
the cytoskeleton dynamics are specific to my parasite at that frequency
across time.

I thought of comparing profiles, like a smooth profile to summarise all
that is happening in each set and test for distances between 2 smoothed
sets. But the timig when something is happening varies a lot, sometimes
it's few seconds, sometimes minutes, sometimes only once per
measurements, sometimes more for the same parasite..
I'm not sure how to proceed.

I have been looking into e1071 package in R for support vector machine,
but I'm not sure this will give me the right model.

I am very grateful for any help / advice anyone can think of

Thank you very much

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