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WGCNA

why Module eigenegene is called first conponent of PCA and why this First component is required in WGCNA. Average gene expression is of a module is not enough for ME caluculation.

pca wgcna eigengene
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written by rajasekargutha • rajasekargutha

It is difficult to assist you, as you have provided minimal information. You will have to expand your question to include code that you have used, results obtained so far, and doubts that you have about what you are doing.

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written by Kevin Blighe Kevin Blighe

i am performing WGCNA for RNA seq data of zebrafish exposed to -10 oc and 28oc. i want to find out which modules are linked to -10oc in zebrafish by WGCNA which uses module and trait correlation functions. i don't have any code problems but I have the understanding problem of wgcna. After the formation of modules, the module eigengene (ME) is calculated which represents with a single value. this module eigenege is called the principal component. My doubt why this is called a principal component. Actually, PCA is issued to reduce the dimension of data. does it mean we reduce the data for ME calculation? why should we reduce it? does it reduces number of samples or number of genes in a module in this step

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written by rajasekargutha • rajasekargutha

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