I am using R studio 3.3.1, and attempting to use 'make.cdf.package' from a cdf for the Clariom_D_Human.r1.Gene.cdf as obtained from Affymetrix and following this tutorial.
after calling 'make.cdf.package'
make.cdf.package("Clariom_D_Human.r1.Gene.CDF", cdf.path = "C:/Users/..../Clariom_D_Human.r1.Gene.CDF", compress = FALSE, species = "Homo_sapiens", package.path = pkgpath)
I get the following error:
"Error in isCDFXDA(file.path(path.expand(cdf.path), filename)):
Unable to open this file C:/Users/.../Clariom_D_Human.r1.Gene.CDF"
I obviously put in the whole path, simply for ease of typing have abbreviated it here. This as a result has made it so that I am unable to process the data or normalize it. I have called both AffyMetrix and the Laboratory whom preformed the MicroArray and was met with "we do not support this on third party programs" and "we couldn't get it to work either so we just used affy expression console" consecutively.
Suggestions of perhaps it is not yet supported by Bioconductor have also come in, but as I am attempting to treat it as a custom CDF this should not be of issue.
Thank you for any help