Question: Co-expression network integration
0
gravatar for pranav
23 months ago by
pranav0
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--

1)WGCNA--

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 • 749 views
ADD COMMENTlink modified 23 months ago by genomax68k • written 23 months ago by pranav0
1

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

ADD REPLYlink written 23 months ago by Deepak Tanwar3.9k

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 23 months ago by pranav0
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