Question: Wgcna-Trait File For Microarray Data
gravatar for pixie@bioinfo
7.0 years ago by
pixie@bioinfo1.4k wrote:

Hi, I am working on plant microarray data in drought condition. I am using WGCNA (R package) for building co-expression modules. In the tutorial, they have mentioned about clinical trait data. I wanted to know what kind of data I can use in my case ? fold change ?..any suggestions will be very much appreciated.

R microarray • 3.7k views
ADD COMMENTlink modified 7.0 years ago by Eric Normandeau10k • written 7.0 years ago by pixie@bioinfo1.4k

Dear Sanchari,

You can find differently expressed genes from your data by limma package and then cluster them by WGCNA. There is a classic example on Yeast Cell Cycle data. I wrote R codes and have required data. Let me know if you are interested.

Best Regards,


Mohammad Hossein Banabazi PhD candidate in Animal Genetics & Breeding (Univ. of Tehran), & Member of Scientific Board

Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), The First Dehghan Villa, Shahid Beheshti St., P.O.Box: 1483, Post Code: 3146618361, Karaj, IRAN. Tel (ASRI): 98-26-34430010 (ext. 467) Tel (Home): 98-26-34470775 Mobile: 98-935-247-0-999 Fax: 98-26-34413258 Alternative E-mail:,, and ID: ooVoo & Skype: banabazi, Yahoo Messenger: mh_banabazi, Google Talk: hossein.banabazi Webpage: CV link:

ADD REPLYlink written 7.0 years ago by hossein.banabazi0

please sir, could you provide r code, i am troubling to match trait data with its expression data

ADD REPLYlink written 4.2 years ago by rajasekargutha30
gravatar for Eric Normandeau
7.0 years ago by
Quebec, Canada
Eric Normandeau10k wrote:

WGCNA is used to create clusters of gene (modules) that are co-expressed among your samples and then to correlate the modules with a trait/condition to find groups of genes that seem to vary in expression with changes in your trait/condition. Finding the co-expression of your modules with fold-change is a strange idea.

I am not sure what this would tell you. You would be trying to find gene modules that vary in expression. I suppose you probably already have a statistical way of finding differently expressed genes from your data.

If I remember well, I think you can use discreet traits, so you could try to correlate with drought condition (drought, no-drought). You can test multiple traits, so even better would be if you had different traits to test. For example: percent of leaves area that is dried (necrosed), millimetres of rain per day, number of days without water, etc.

ADD COMMENTlink written 7.0 years ago by Eric Normandeau10k

Thanks for the insight..the tutorials don't say much about the trait file. I'll try using the discreet trait that you mentioned about..

ADD REPLYlink written 7.0 years ago by pixie@bioinfo1.4k

Hi! So in the case of drought/non-drought, one can create modules separately and afterwards compare the modules in the two conditions? eg.find modules which have same expression patterns?
Or should create modules using both conditions together?

ADD REPLYlink written 6.4 years ago by bioLife50
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