Empirical Bayesian kriging implementation and usage.

We described the key features of the pragmatic geostatistical methodology aiming at resolving the following drawbacks of classical geostatistical models: assuming that the data is the realization of a stationary process; assuming that the data values are distributed according to Gaussian distribution; describing the data with a single generating model; not accounting for the model uncertainty in prediction; and not supporting coincident data and individual measurement errors. Our variant of empirical Bayesian kriging (EBK) is a fast and reliable solution for both automatic and interactive data interpolation. It can be used for interpolation of very large datasets up to billions of points.

Comparing Clusterings Using Bertin's Idea.

Classifying a set of objects into clusters can be done in numerous ways, producing different results. They can be visually compared using contingency tables, mosaicplots, fluctuation diagrams, tableplots, (modified) parallel coordinates plots, Parallel Sets plots or circos diagrams. Unfortunately the interpretability of all these graphical displays decreases rapidly with the numbers of categories and clusterings.

Molecular characterization of AML with ins(21;8)(q22;q22q22) reveals similarity to t(8;21) AML.

In acute myeloid leukemia (AML), nonrandom clonal chromosome aberrations are detectable in ∼ 55% of adult cases. Translocation t(8;21)(q22;q22) resulting in the 5'RUNX1/3'RUNX1T1 fusion gene occurs in ∼ 8% of AML cases. Also, ins(8;21) and ins(21;8) have been described that show a broad heterogeneity at the molecular level with inserted fragment sizes ranging from 2.

SEURAT: visual analytics for the integrated analysis of microarray data.

Background: In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required.

Results: We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data.