GDCRNATools package

Question

[Maryam]

Hello everyone, would you mind helping me? I am using GDCRNATools R package for ceRNA network analysis but I get error. I have 191 lncRNAs, 202 mRNAs, 393 lnc&mRNA expression matrix with 412 samples and 389 miRNAs expression matrix with 446 samples. The code I run is :

 ceOutput <- gdcCEAnalysis(lnc       = lnc2, 
                      pc          = mRNA2, 
                      lnc.targets = 'starBase', 
                      pc.targets  = 'starBase', 
                      rna.expr    = RNAEX, 
                      mir.expr    = mirexpr)

but I get this error:

Step 1/3: Hypergenometric test done !

Error in cor.test.default(lncDa, mirDa, alternative = "less") : 
  not enough finite observations

[bk11]

What are your lnc2 and mRNA2? I would recommend you to make sure that you do not have NA in your input.

[Maryam]

Thanks for your reply. lnc2 is the vector of 191 lncRNA ensembl ids and and mRNA2 is the vector of 202 mRNA ensembl ids. There are no NAs as far as I have checked. The expression matrices are data that I have obtained from TCGA and I filtered and normalized the raw expression data by TMM method.