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What file formats requires for WGCNA ??

I am unable to understand how to perform WGCNA analysis in R. I am facing difficulties fo this network analysis

r gene
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updated by WouterDeCoster WouterDeCoster • written by Santosh • Santosh

Did you check their manual/tutorial page here ?

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written by venu venu

Hello Santosh!

We believe that this post does not fit the main topic of this site.

This thread shows insufficient input of the OP to solve this problem himself. The manual and tutorial of WGCNA is one of the best you can find. I agree that it might take a while to get comfortable with the package, but that is no reason to cut corners and just have someone on the internet do your work. If you have more specific questions feel free to open a new thread.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by WouterDeCoster WouterDeCoster

1 answer

Have you looked at WGCNA documentation? https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/

Generally speaking, the initial input is a "properly normalized" gene expression matrix where rows represent genes and columns represent samples. Proper normalization depends on the platform used. In case of microarrays, the limma package from Bioconductor provides several methods for array normalization. In case of RNAseq, you can obtain normalized counts (or RPKM/FPKM/TPM data) and log-transform them, or better yet use a variance-stabilizing method such as VST or rlog provided by DESeq2 (also from Bioconductor).

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written by sina.nassiri • sina.nassiri

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