I would like to use the 'Ax2APT' function from 'affy2sv' package in Horse Axiom files. That´s how my code look like:

library(affy2sv)
Ax2APT( 
  cel.files="/home/user/rawData/Axiom_Horse/Axiom_MNEc670",
  output.path="/home/user/penncnvData", 
  analysis.path="/home/user/libraryData",
  xml.dqc=" Axiom_MNEc670.r1.apt-geno-qc.AxiomQC1.xml", 
  xml.config.1="Axiom_MNEc670_96orMore_Step1.r1.apt-probeset-genotype.AxiomGT1.xml", 
  xml.config.2="Axiom_MNEc670_96orMore_Step2.r1.apt-probeset-genotype.AxiomGT1.xml")

However, I am getting this error:

Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file 'tmp.ax.apt.75854750511.1': Permission denied

The folder exist and I have permission to write and read there. Some idea?

That's not a Bioconductor package, so you need to ask the author directly.