Error related to matrix system is exactly singular

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Error related to matrix system is exactly singular

anikaM
Hello,

I was running this software https://github.com/eleporcu/TWMR
via:

Rscript MR.R ENSG00000154803
my files are located here:
https://filebin.net/smt1kcw2d9sody67

I got this error:

[1] "ENSG00000154803"
Error in solve.default(C) :
  Lapack routine dgesv: system is exactly singular: U[15,15] = 0
Calls: solve -> solve.default
Execution halted

in the original code I changed this:

and I also in order to run it I changed the beginning of the code to be:

cmd_args <- commandArgs(TRUE)if (length(cmd_args) == 0L) stop("No
arguments specified.")
print(cmd_args)
gene<-cmd_args[length(cmd_args)]   ## Last argument is the 'gene'
Ngwas<-239087
N_eQTLs<-32000
out<-c("gene","alpha","SE","P","Nsnps","Ngene")

file<-paste(gene,"matrix",sep=".")if (!file.exists(file)) stop("File
not found: ", file)
filecluster<-read.table(file,header=T,sep=" ",dec=".")
beta<-as.matrix(filecluster[,2:(length(filecluster[1,])-1)])

when I was running it with just 3 columns in .matrix file.

Please advise, is it something wrong with the format of my files now?

Thanks

Ana

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Re: Error related to matrix system is exactly singular

Jeff Newmiller
See below

On December 4, 2019 10:04:45 AM PST, Ana Marija <[hidden email]> wrote:
>Hello,

... removed for clarity

>
>Please advise, is it something wrong with the format of my files now?
>
>Thanks
>
>Ana
>
> [[alternative HTML version deleted]]

...

>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

You are sabatoging your own efforts to get help by repeatedly posting HTML- formatted email on a plain- text-only mailing list.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.