Question: error in WGCNA
0
gravatar for nazaninhoseinkhan
2.0 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan360 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"

 library(flashClust)
> 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

Nazanin

adjacency error wgcna • 998 views
ADD COMMENTlink modified 24 months ago by Biostar ♦♦ 20 • written 2.0 years ago by nazaninhoseinkhan360
1

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

ADD REPLYlink written 2.0 years ago by Jake Warner680

Hi

Yes. there are gene symbols in multiExpr

ADD REPLYlink written 2.0 years ago by nazaninhoseinkhan360

Well there's your problem.

ADD REPLYlink written 2.0 years ago by WouterDeCoster37k

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 2.0 years ago • written 2.0 years ago by Jake Warner680
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