Summarising WGCNA data with modules and their corresponding gene ID and statistics
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synat.keam • 0
@1d56a66c
Last seen 2 days ago
Australia

Dear All,

I'm analysing my RNASeq data using WGCNA to identify genes that are co-expressed and detect modules, correlating with traits. I have done most of the analysis and identify the modules and examined the association of the modules with traits successfully. Next is to generate a summary, which contains modules with their corresponding gene ID/name and statistics.

I have normalized count data from DESeq2 with row for genename and column for sampleID. I do not have any other annotation file except the trait file, which is different dose of radiation treatment. I have attached the data frame

The code chunck provided in WGCNA tutorial mostly convern with microarray data and it has a comprehensive list of annotation file and I have attached the code from the tutorial in the following

I do not have probe information, locus linkID, but only the geneID/name in the count matrix. Is there any way I could simply generate a summary with just gene name/ID in the normalized count matrix I have attached? Looking forward to hearing from the WGCNA author and others who had experience analysing WGCNA.

Kind REgards,

synat

# please also include the results of running the following in an R session

sessionInfo( )

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RNASeq WGCNA • 91 views
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Okay, I have successfully solved the problem. If anyone experienced the same issue, let me know.

Cheers,