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 Celine -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
Dear Celine If you are considering using support vector machines in R, you might find it worthwhile to read the paper: http://www.jstatsoft.org/v15/i09/paper Best, Niels Celine Carret wrote:> 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 > Celine > > > >-- Niels Richard Hansen Associate Professor Department of Mathematical Sciences University of Copenhagen Universitetsparken 5 2100 Copenhagen ? Denmark +45 353 20783