Question: WGCNA error help
0
gravatar for Azhar
2.7 years ago by
Azhar40
China
Azhar40 wrote:

I have two files for two diff conditions having lncRNA and mRNA expression values combined in each file i want to make interaction networks when i go through example it owrks well but when i use my data sample it gives several errors and problem like

1.

> sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)
pickSoftThreshold: will use block size 773.
 pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 773 of 57862
Error in { : task 1 failed - "'x' has a zero dimension."
> # Plot the results:
> sizeGrWindow(9, 5)


2.Error in plot(sft$fitIndices[, 1], -sign(sft$fitIndices[, 3]) * sft$fitIndices[,  : 
  object 'sft' not found
> text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
+      labels=powers,cex=cex1,col="red");
Error in text(sft$fitIndices[, 1], -sign(sft$fitIndices[, 3]) * sft$fitIndices[,  : 
  object 'sft' not found

3Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'GeneAnnotation.csv': No such file or directory

.4.Error in exportNetworkToCytoscape(modTOM, edgeFile = paste("CytoscapeInput-edges-",  : 
  Cannot determine node names: nodeNames is NULL and adjMat has no dimnames.

rna-seq • 1.7k views
ADD COMMENTlink modified 2.7 years ago by RamRS24k • written 2.7 years ago by Azhar40
1

The error originates in pickSoftThreshold(). Make sure that datExpr and powers are the objects you expect them to be. In addition, using WGCNA as a tag for your question would make sense. I'm also not sure why your question would be urgent (or more urgent than other questions).

ADD REPLYlink written 2.7 years ago by WouterDeCoster42k

urgent means as soon as possible its just a request any how thanks for reply can you please guide me if I don't want to use clinical data how I can modify this WGCNA code for network construction for simple data file and what is meant by

-x has no dimension error

I am running the code as it is just changing the file name so this error appears

ADD REPLYlink written 2.7 years ago by Azhar40

I've removed the term "urgent" from your question. Please do not use words like "urgent" or "emergency" - they don't help your case.

ADD REPLYlink written 2.7 years ago by RamRS24k
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