Question: error in WGCNA
gravatar for nazaninhoseinkhan
2.8 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan390 wrote:

Dear all,

I am trying to use WGCNA to find consensus modules between two species.

But when I want to build the adjacency matrix I get the following error"

> load(file="Consensus-dataInput.RData")
> nSets = checkSets(multiExpr)$nSets
> softPower1 = 6;
> softPower2 = 6;
> adjacencies = array(0, dim = c(nSets, nGenes, nGenes));
> set=1
> adjacencies[set, , ] = adjacency(multiExpr[[set]]$data, power = softPower1,type= "signed hybrid");
**Error in cor(datExpr, use = "p") : 
  REAL() can only be applied to a 'numeric', not a 'character'**

Can anybody guide me what should Ido to solve this problem?

Thank u in advance


adjacency error wgcna • 1.3k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 2.8 years ago by nazaninhoseinkhan390

Are there non-numeric entries in multiExpr? For example gene IDs?

ADD REPLYlink written 2.8 years ago by Jake Warner780


Yes. there are gene symbols in multiExpr

ADD REPLYlink written 2.8 years ago by nazaninhoseinkhan390

Well there's your problem.

ADD REPLYlink written 2.8 years ago by WouterDeCoster42k

Wouter is correct. Move your gene symbols and sample names into the rownames or colnames respectively (depending on the orientation of multiexpr) and try again.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Jake Warner780
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 873 users visited in the last hour