Experimental data

We used the BDNF dataset published by Gurok et al. (6). In that study, neural progenitor cells were prepared from postnatal day 7 CD1 mice (Charles River, Wilmington, Mass.) and their differentiation process was examined. For comparison of normalization methods, we only used the experimental data of undifferentiated cells and the first day of differentiation with BDNF. This data consists of one dye-swap experiment, so two arrays were used, and signal intensities of two laser channels were measured per array. The data is available as supplementary information to the publication (http://www.molgen.mpg.de/~dna_microarrays-neural_differ-entiation/neural.html). This data serves as an example of a high number of genes showing a very low expression.

As a second example we used a gene expression dataset from the swirl zebrafish cDNA microarray experiment which is available in the Bioconductor (22) Marray-package. The dataset consists of two dye-swap experiments of which we used the first array (slide 81). It serves as an example of nonlinearity of microarray data.

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