Back in mid-July, I manually created modules to cluster genes by expression patterns. Again, “manual” oversells it a bit - I really just provided a cut height, looked at the resulting clusters, and then named them by overall expression patterns. A recap of that naming system can be found in my lab notebook entry on 2021-07-12 (named Manual Modules 3)
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Crab Plasticity
In our previous post, we created PCAs for each transcriptome, with each point as one library. This raised some interesting questions, notably that we didn’t necessarily see libraries from the same crab clustered together (though for some crab, they did clearly cluster). This could be an indication of crab plasticity, as they adjust to both tank effects and the temperature treatment.
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Creating PCAs
Alright, as of last time, our general goal was to do the following (along with a few other priorities):
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Manual Modules 3
UPDATE: Changed the bar for gene expression by 2021-08-09. Protocol was the same otherwise For more info, refer to the lab notebook post for Aug. 9th, 2021
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WGCNA Part 3
Success!!
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