Error in svd(X) : infinite or missing values in 'x'

[xiaowei3223]

Hi, Zhang Yun,

when I used my data via FUNNEL.GSEA, I don't know what's problem in my data. Can you help me to solve this problem.

my data is at this link .

codes are:

load("xd.RData")
genesets = qusage::read.gmt("c2.cp.kegg.v7.0.symbols.gmt")
t <- c(0,6,30)
Y <- FUNNEL.GSEA(xd, t, genesets)

And it shown me is:

22 real eigenvalues are negative or zero and are removed!
Error in svd(X) : infinite or missing values in 'x'
In addition: Warning messages:
1: In interpp.old(x, y, z, xo, yo, ncp = 0, extrap = FALSE, duplicate = duplicate,  :
  interpp.old() is deprecated, future versions will only provide interpp()
2: In interpp.old(x, y, z, xo, yo, ncp = 0, extrap = FALSE, duplicate = duplicate,  :
  interpp.old() is deprecated, future versions will only provide interpp()
3: In sqrt(romb2(out1, phi[, i]^2)) : NaNs produced

When I test whether my data have NA:

table(is.na(xd))
#FALSE 
#56496 

Thank you!

Your sincerely,
Xiaowei

-email: [email protected]