Error in eigen using VEGAS

Question

[hallie.cla]

Hello,

I'm trying to run a gene-set based analysis using VEGAS, a software that calls PLINK and R, and uses HapMap to estimate patterns of linkage disequlibrium for each gene. I just followed the basic format ./vegas [input file] -pop hapmapCEU and I received this error:

Error in eigen(m, only.values = TRUE, symmetric = TRUE) : 0 X 0 matrix
Calls: is.positive.definite -> eigen
Execution halted

Do you have any idea on what might be causing this error and how could I correct it?

Thanks a lot

Claudia

[Jean-Karim Heriche]

It fails because it didn't get a matrix with data. This is indicated by '0 x 0 matrix'. Investigate why eigen() is not receiving a matrix with data.

[Shicheng Guo]

Have you ever try other gene-set approach? for example, rvtest