Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

Projects within DNA microarray



Teacher:

  • Carsten Friis


    Overview of Lectures:

    • Tuesday 14/3
    • DNA microarray technology (Test) (Answers); Basic UNIX and R (Test) (Solutions)
      Pensum: Kapitel 13, p.612 - p.628
    • Tuesday 21/3
    • Normalization and statistics (Exercise)
      Pensum: Kapitel 13, p.628 - p.637 (til 'Distance-based Methods')
    • Tuesday 28/3
    • Advanced Data Analysis (Exercise)
      Pensum: Kapitel 13, p.637 - p.658
    • Tuesday 4/4
    • No lecture => free for writing
    • Tuesday 18/4
    • No lecture => free for writing
    • Tuesday 25/4
    • No lecture => free for writing
    • Tuesday 2/5
    • No lecture => free for writing
    • Tuesday 9/5
    • Hand in reports to Carsten Friis before 17:00 (Use mailbox next to room 010, CBS, Building 208)

    The final report

    (The data sets described on this site are not public and may only be used for project work)

    Bladder cancer dataset:

    To obtain the individual chip files, you need a CBS account. You can copy the files to your databar account (log into a Unix machine like bohr) with this command:
    scp myusername@genome.cbs.dtu.dk:"/home/people/steen/genemachine/bladder/*.CEL.gz" .
    
    where myusername is your account name on genome and the period at the end of the line is very important (it means copy the files to here).

    HIV dataset:

    To obtain the individual chip files, you need a CBS account. You can copy the files to your databar account (log into a Unix machine like bohr) with this command:
    scp myusername@genome.cbs.dtu.dk:"/home/people/steen/genemachine/hiv/*.CEL.gz" .
    
    where myusername is your account name on genome and the period at the end of the line is very important (it means copy the files to here).

    Leukemia dataset:

    • GenePublisher report of T versus B cell leukemia
    • Results of testing a classifier to predict outcome (relapse versus remission) on an independent test set
    To obtain the individual chip files, you need a CBS account. You can copy the files to your databar account (log into a Unix machine like bohr) with this command:
    scp myusername@genome.cbs.dtu.dk:"/home/people/steen/genemachine/leukemia/*.CEL.gz" .
    
    where myusername is your account name on genome and the period at the end of the line is very important (it means copy the files to here).


    Further analysis

    You can run your own analysis through the GenePublisher website. Note, however, that the analysis may take hours and that a single mistake in the input will cause the analysis to fail.

    You can also run your own analysis on the command line provided you have a CBS account on genome. See the manpage 'cbsman genepublisher' for details.