Multi-omics studies can highlight the interrelationships among data across different layers of biological information. However, methods for the unsupervised analysis of multi-block data do not take the individual variability across batches into account and cannot deal with omics datasets when they present different numbers of replicates. We have explored three different data arrangement strategies to tackle these limitations. Several multi-block methods can be used to decipher the common variations across blocks and to determine the contribution of each block to each common component. In this study the ComDim method was used to compare these rearrangement strategies for three multi-omics datasets. We found that arranging the data using the ‘replicate by blocks’ strategy, where each block comprises data from only one replicate independently of its data type, provided the most insightful results. ComDim allowed the evaluation of the variability across the replicate blocks, confirming the existence of batch effects in some of the studies. Moreover, since the contributions of these batch effects were separated from the other contributions, the coordinated biological responses common across the different blocks was characterized for each data type.