Reading Clariom D Human CEL files results in missing CDF enviroment error

Question

[jonifg]

Hello!

I am trying to analyze CEL files for the Clariom D human platform (Clariom_D_Human). Trying to use the ReadAffy function or read.celfiles from oligo, both result in a missing CDF enviroment error.

batch = ReadAffy(filenames = celFiles, phenoData = phenodata)

"missing cdf environment! in show(AffyBatch)"ERROR while rich displaying an object: Error in getCdfInfo(object): Could not obtain CDF environment, problems encountered: Specified environment does not contain clariomdhumanhsgenecodegcdf Library - package clariomdhumanhsgenecodegcdf not installed Bioconductor - clariomdhumanhsgenecodegcdf not available

Of course I haven't found the clariomdhumanhsgenecodegcdf, I've also tried with the argument cdfname = 'pd.clariom.d.human' (in case the platform description would be useful here) but this doesn't work either.

I found a custom CDF package in [http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/genecodeg.asp][1] but I am unable to properly install it or call it.

How can I install this enviroment?/Load the batch?

Thank you for the help!

Answer 1

[R.Blues]

Mmmmm. Have you tried taking a look at their CustomCDF package? Maybe there is something on it that you can use http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v22

Please let us know if that worked! :)