Question: WGCNA extract genes from a module
0
gravatar for bdy8
13 months ago by
bdy80
bdy80 wrote:

Hi there everyone

I am only posting this question as every other response to this topic suggest to use an example from a website which, using many different sources, I get a 404 error or site not found. This common answer site is posted below

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-04-Interfacing.pdf 

As such, I have performed a WGCNA analysis using this tutorial. 

https://wikis.utexas.edu/display/bioiteam/Clustering+using+WGCNA 

The last line says to extract modules as such from the data analysis (datExpr = normalized counts file output from DESeq2)

topGOgenes <- names(datExpr)[moduleColors=="brown"]

With this, however, I get "no data avaliable in table".

I understand this is probably a very basic fix/command but I have hit a wall in working it out for myself (be that using resources or my pior Rprogramming skills). 

Any and all help is really apreciated and thank you in response. 

 

Ben

wgcna wgcna package • 566 views
ADD COMMENTlink modified 13 months ago by Peter Langfelder2.2k • written 13 months ago by bdy80
Answer: WGCNA extract genes from a module
1
gravatar for Peter Langfelder
13 months ago by
United States
Peter Langfelder2.2k wrote:

Regarding the WGCNA website, sorry for the missing files, here's the new address:

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/

You can follow the tutorial there. Extracting the genes in a module is described in Tutorial I, section 3d.

Peter

 

 

ADD COMMENTlink written 13 months ago by Peter Langfelder2.2k

Hi Peter

Thank you so much. I was not able to find your new site for the life of me. 

It is all working now.

Have a great Friday and weekend. 

ADD REPLYlink written 13 months ago by bdy80
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