Figure 1

MDS plots. Visual inspection of two merged data sets using double-labeled Multi Dimensional Scaling (MDS) plots. In these MDS plots samples are labeled by color based on the target biological variable of interest and are labeled by symbol based on the study they originate from. On the left the two data sets are merged without any transformation and on the right the two data sets are merged by using the COMBAT method. It is intuitively clear from the MDS plots that samples cluster by study without any transformation and by disease after performing COMBAT.