Hi,
what is the minimum number of samples to run OmicsAnalyst?
Can samples from the same tissue but from different species be analysed together?
This is a tricky question and the answer depends on your analysis path. We discussed this topic in our recent [Nature Protocol] (Web-based multi-omics integration using the Analyst software suite | Nature Protocols), see Box 1 . The most related sections are given below:
Sample matching
Different omics data should ideally be collected from the same set of biological samples. The requirement is essential for data-driven integration, which aims to identify shared patterns and correlated molecular features directly based on the omics data themselves. Knowledge-driven integration is much more flexible as omics signatures can be obtained from related but independent samples. Much existing knowledge is about interactions at molecular and cellular level, for example, PPIs or metabolic reactions. It is important to keep in mind that different omics layers operate at very different time scales, which could have a large effect on the measured correlations83. The relevance of this knowledge to our multi-omics studies depends on how physically and temporally close they are to each other, and the overall analysis context.
Sample size
Certain methods do not give robust results with smaller sample size21,59. In general, we recommend at least 20 samples per group for performing DR analysis. In addition, differences in statistical power based on sample size relative to the variations associated with the underlying omics platforms should be considered when comparing and integrating results. One omics layer having more significant features does not necessarily mean that that it is more biologically relevant, but rather could reflect superior technical performance of the platform.