WGCNA extract genes from a module
1
1
Entering edit mode
bdy8 ▴ 10
@bdy8-16982
Last seen 5.8 years ago

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 • 5.6k views
ADD COMMENT
1
Entering edit mode
@peter-langfelder-4469
Last seen 7 weeks ago
United States

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 959 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6