How to perform differential gene expression analysis for rna seq between two different sets
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Hello friend ❤️
To explain, suppose for a moment that even when specific transcripts / isoforms change, gene co-expression patterns acting coordinately to subserve the same goals change less in related organisms.
If the co-expression networks you generate after assembly are highly similar, you would have in essence provided yourself a data-driven validation that this approach produced sensible results (that you could then use to wade through various possibilities you mention in 1-6).
Hope helps ❤️
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