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rli012 / GDCRNATools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC
Apache License 2.0
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Error in gdcCEAnalysis: not enough finite observations #14

Open NatashaJorge opened 4 years ago

NatashaJorge commented 4 years ago

Hello!

my name is Natasha and I am following the tutorial on http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNATools/inst/doc/GDCRNATools.html#cernas-network-analysis-of-degs

I have 273 miRNAs and mRNAs on my expression table. However, when I give the following command:

ceOutput <- gdcCEAnalysis(lnc = rownames(deLNC), pc = rownames(dePC), lnc.targets = 'starBase', pc.targets = 'starBase', rna.expr = mrna2, mir.expr = mirna2)

It gives me this error:

Step 1/3: Hypergenometric test done ! Error in cor.test.default(lncDa, mirDa, alternative = "less") : not enough finite observations

there are 99 deLNC and 1622 dePC (FDR <= 0.05)

Please, can you help me? Where did I do wrong?

best wishes, Natasha

MaiTian-li commented 3 years ago

Hello! I have encountered the same error, do you know how to resolve this issue now? Thanks for your reply!