Question: WGCNA analysis for normalised data expression data sets
0
gravatar for krushnach80
9 weeks ago by
krushnach80170
krushnach80170 wrote:

I am looking for WGCNA script , there is something in the script called "traitData" what exactly it is?

What i have is normalised data sets, but i dont have the "traitData" ,do i need to have "traitData" to do WGCNA ?analysis

rna-seq • 154 views
ADD COMMENTlink modified 9 weeks ago by amy.bashir60 • written 9 weeks ago by krushnach80170
2
gravatar for amy.bashir
9 weeks ago by
amy.bashir60
amy.bashir60 wrote:

Trait data is biological features associated with each animal that the sample is derived from. For example, if you are studying the gene co-expression networks underlying a cardiovascular disease, trait data would be the things like weight, blood pressure and blood cholesterol level of each patient/animal that you got the the RNA sample from.

Providing trait data allows you to calculate gene and module significance, thereby gaining insights into the relative "biological significance" of a gene or an interesting module to whatever you are studying.

I don't think you need trait data to do WGCNA, but it would allow you to get more out of it.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by amy.bashir60

so i have data from blood cell development from various stages ,so i dont need the trait data or do I ?

ADD REPLYlink written 9 weeks ago by krushnach80170

Well, trait data can be added in later if you find a particular module of interest and think that it could be correlated with a trait that you are seeing (just my random guess, like if you are seeing variations in how well each sample is "developing").

Integrating trait data basically allows you to find genes or modules that play a more decisive role in the process that you are studying. In the example above, it would be like finding which genes or modules play the most important role in determining the risk/severity of cardiovascular disease.

ADD REPLYlink written 9 weeks ago by nancydong2060
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