lines indicate the median. [**Bottom row:**]{} Only the five Affymetrix data sets were used in the paired setting.[]{data-label="fig:boxplot_pw_vs_merged"}](Plots/Doxplot_Experiment_08_AFFYmerged_50_features.pdf "fig:"){width="3in"}\

pairwise

& ![**Classification results for merged and paired setting**. In the merged setting one Affymetrix data set is set aside as test and the remaining four Affymetrix data sets are merged into a single data set. This is repeated until every one of the five data sets acted as a test set. [**Top row:**]{} Results for the merged setting. The red lines indicate the median. [**Bottom row:**]{} Only the five Affymetrix data sets were used in the paired setting.[]{data-label="fig:boxplot_pw_vs_merged"}](Plots/Boxplot_Experiment_07_NMCv1.pdf "fig:"){width="3in"} & ![**Classification results for merged and paired setting**. In the merged setting one Affymetrix data set is set aside as test and the remaining four Affymetrix data sets are merged into a single data set. This is repeated until every one of the five data sets acted as a test set. [**Top row:**]{} Results for the merged setting. The red lines indicate the median. [**Bottom row:**]{} Only the five Affymetrix data sets were used in the paired setting.[]{data-label="fig:boxplot_pw_vs_merged"}](Plots/Boxplot_Experiment_07_50_features_NMCv1.pdf "fig:"){width="3in"}\

### Dataset homogeneity affects single genes and composite classifiers similarly {#dataset-homogeneity-affects-single-genes-and-composite-classifiers-similarly .unnumbered}

Breast cancer is a collection of several heterogeneous diseases that 