Hello,
I am trying to use the TCGAvisualize_SurvivalCoxNET function on my data, but it keeps throwing an error,
Error in wilcox.test.default(within.degrees, cross.degrees, ...) : not enough (non-missing) 'x' observations In addition: Warning message: In dNetFind(g, scores) : No positive nodes
Error in wilcox.test.default(within.degrees, cross.degrees, ...) : not enough (non-missing) 'x' observations In addition: Warning messages: 1: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Loglik converged before variable 1 ; coefficient may be infinite. 2: In dNetFind(g, scores) : No positive nodes
I am not quite familiar with igraph so unable to solve why this keeps happening. The previous steps are working fine though!
Hello, I am trying to use the
TCGAvisualize_SurvivalCoxNETfunction on my data, but it keeps throwing an error,Error in wilcox.test.default(within.degrees, cross.degrees, ...) : not enough (non-missing) 'x' observations In addition: Warning message: In dNetFind(g, scores) : No positive nodesI tried running it on test data as done in the manual here https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/casestudy.html, for BRCA data, it gives the same error:
Error in wilcox.test.default(within.degrees, cross.degrees, ...) : not enough (non-missing) 'x' observations In addition: Warning messages: 1: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Loglik converged before variable 1 ; coefficient may be infinite. 2: In dNetFind(g, scores) : No positive nodesI am not quite familiar with igraph so unable to solve why this keeps happening. The previous steps are working fine though!