error in WGCNA

Question

[nazaninhoseinkhan]

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

[Jake Warner]

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

[nazaninhoseinkhan]

Hi

Yes. there are gene symbols in multiExpr

[WouterDeCoster]

Well there's your problem.

[Jake Warner]

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.