Question: Co-expression network integration
gravatar for pranav
2.8 years ago by
pranav0 wrote:

Hi ,I am new to R as well as computational biology. I am having expression profiles for lncRNA and mRNA of capsicum species . All I want to do is annotate the novel lncRNAs. How do I do that? I read about WGCNA as well as LncPath. However I few doubts--


Do we require the "clinical traits file" as mentioned in the tutorial for constructing the network? If no, can anyone help me with network construction..?

Also I get lot of error in step 2 of network contruction like

Error in { : task 1 failed - "'x' has a zero dimension." 
and many....

2)For LncPath When i use the getnet function for my input file and display the result, it shows result only from example file and not from input file. Also when i searched on Internet about get-net function it says it is from mlVAR package. I installed that too,but no success.

How do i generate co expression network for lncRNA-mRNA and integrate it with PPI data and then annotate it?

Would be grateful if anyone helps!

rna-seq wgcna • 1.0k views
ADD COMMENTlink modified 2.8 years ago by genomax83k • written 2.8 years ago by pranav0

Put the code that you used for doing analysis and the step where you got error.

ADD REPLYlink written 2.8 years ago by Deepak Tanwar4.0k

I get error in the following step:

sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5) pickSoftThreshold: will use block size 2895. pickSoftThreshold: calculating connectivity for given powers... ..working on genes 1 through 2895 of 15450 Error in { : task 1 failed - "'x' has a zero dimension."

also would like you to know that my file will not contain results from the "clinical traits file" since i dont want it. My input file is 'Sample_input.RData' obtained by execution of 'Data input cleaning' step as per WGCNA tutorial. It contains only "datExpr" because I omitted the code chunk that is used for processing of "clinical traits" file.

Ex. lnames = load(file = "Sample_input.RData"); lnames datExpr"

ADD REPLYlink written 2.8 years ago by pranav0
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