Hi everyone,
Im quite new to co-expression network analysis and I've been wondering what would be the minimum time points I could use to create a meaningful co-expression network to analyze? I currently have 2 time points with 8 samples each but after reading around it seems 3 might be the minimum? Is that true, do I need more than 3, or could I extract meaningful information from 2 timepoints? On a similar note is there any publication I might be missing where this is stated? Thank you!
Are you planning to use some particular tool to infer the co-expression network? If you're using a tool, they often provide recommendations on sample size in their documentation. For example, WGCNA suggests no less than 15 samples while ARACNe recommends at least 100. While those are two of the most popular co-expression inference tools, they do not leverage the longitudinal information you have with timepoints. Do you have a plan for leveraging your longitudinal information?
Side note: it is also very important to consider appropriate normalizations and transformations for your transcriptomic data. Do you have a plan for that?
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