Non-linear PCA: a missing data approach.
BACKGROUND
Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values.


RESULTS
Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while optimizing the model, but can be estimated afterwards. Results are shown for both artificial and experimental datasets. In contrast to linear methods, non-linear methods were able to give better missing value estimations for non-linear structured data.


CONCLUSIONS
We applied this technique to a time course of metabolite data from a cold stress experiment on the model plant Arabidopsis thaliana, and could approximate the mapping function from any time point to the metabolite responses. Thus, the inverse NLPCA provides greatly improved information for better understanding the complex response to cold stress.


BACKGROUND
scholz@mpimp-golm.mpg.de.
Scholz
Matthias
M
Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
Kaplan
Fatma
F
Guy
Charles L
CL
Kopka
Joachim
J
Selbig
Joachim
J
D000222:Adaptation, Physiological / Q000502:physiology; D000465:Algorithms; D017360:Arabidopsis / Q000502:physiology; D029681:Arabidopsis Proteins / Q000378:metabolism*; D003080:Cold Temperature; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D008957:Models, Genetic; D015233:Models, Statistical; D017711:Nonlinear Dynamics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D025341:Principal Component Analysis; D015398:Signal Transduction / Q000502:physiology
D029681:Arabidopsis Proteins