Project work 

The idea is to make a small scale research project that will give you
some hands-on experience on analysis of metabolomic data. You do not
have to get outstanding results, but if you do, we will contact you
and suggest a writing of a scientific paper. :-)  

The data is on DVD, and can be borrowed for a short while from Janne
Nikkilä, room A336. There is a brief documentation about the data sets
included in the DVD.

The easiest way to get started is to use MZmine
(http://mzmine.sourceforge.net/) to import the data (or a subset of
it), preprocess it, and export it as tab-delimited textfile that can
be imported into R or Matlab, or any other analysis platform of your
choice. NOTE: There will be a new version of MZmine available on
Tuesday 29.11., which should be used instead of the current
one. MZmine requires the newest version of java, for example, in
Macintosh, after installing the new java (see
http://developer.apple.com/java/), you have to specify the full path
if you have the old one as a default version (see
http://developer.apple.com/releasenotes/Java/Java50Release3RN/index.html). In
other systems, the new java is assumedly the default after the
installing.

You are expected to understand and to be able to justify the choices
made in the preprocessing, and then to conduct some relevant (small
scale) data analysis of the data (some relevant clustering, use of
linear models, classification, feature extraction, etc.).

The report should resemble a small conference paper. It should
describe the overall goal, the choices, their justifications, the
methods and the results with relevant illustrations in max. 6 pages,
but it can be shorter. The amount of credits is approximately 2.5 from
this project work, so try to scale the amount of work according to
that. The project corresponds feasibility studies conducted in most
research groups, and the aim is to get results that give an overview
of the data and the problem, and help to make the decision whether to
continue the research on that subject. We would suggest for example
following resource allocation: 2 days to get acquinted with the data,
MZmine, and to preprocess the data, 1.5 days for planning the
analysis, 2.5 days to make the analysis, and 2 days for writing the
report. The deadline for the report is 15th of January 2006.