Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps

doi:10.1186/1748-7188-3-9

Algorithms for Molecular Biology

Volume 3

Viewing options:

Abstract
Full text
PDF (402KB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Meinicke P
Lingner T
Kaever A
Feussner K
Göbel C
Feussner I
Karlovsky P
Morgenstern B

on PubMed

Meinicke P
Lingner T
Kaever A
Feussner K
Göbel C
Feussner I
Karlovsky P
Morgenstern B
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Research

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps

Peter Meinicke¹ , Thomas Lingner¹ , Alexander Kaever¹ , Kirstin Feussner² , Cornelia Göbel³ , Ivo Feussner³ , Petr Karlovsky⁴ and Burkhard Morgenstern¹

¹Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany

²Department of Developmental Biochemistry, Institute for Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany

³Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany

⁴Molecular Phytopathology and Mycotoxin Research Unit, University of Göttingen, Göttingen, Germany

author email corresponding author email

Algorithms for Molecular Biology 2008, 3:9doi:10.1186/1748-7188-3-9


Published:	26 June 2008

Additional files

Additional file 1:

Movie of the annealing process during clustering. The file cluster_process_33nodes.mpg contains a movie that shows the annealing process during clustering of the experimental data used in our case study. The annealing schedule realizes an exponential decrease of the smoothing parameter σ over 100 steps. The initial value is σ_max= 100 and the final value is σ_min= 0.1.

Format: MPG Size: 622KB Download file

Playing the movie within this page requires QuickTime 6.4 or later and JavaScript. Read more

Additional file 2:

List of MarkerLynx™ parameters. The data file MarkerLynxParameters.xls contains an Microsoft^®Excel table with parameters that were used for data preprocessing with MarkerLynx™.

Format: XLS Size: 8KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Table of marker candidates used in the case study. The data file dataset837.csv contains the marker candidates used for clustering and visualization. Rows correspond to particular marker candidates. The first column corresponds to marker candidate ID, the second and third column represent cluster ID and block ID according to table 2, respectively. The block IDs A, B, C, D, E and F are encoded by integers 1,..., 6. Columns 4 and 5 correspond to experimental nominal mass (m/z) and retention time (minutes), respectively. Columns 6 to 77 contain intensity values from mass spectrometry measurements. Here, nine successive values correspond to replicas of a particular experimental condition (see section "Case study for experimental evaluation"). The intensity values are ordered according to successive replicas for each condition (order of conditions according to table 1).

Format: CSV Size: 645KB Download file