Hi

I'm new to processing microarray data and new to Robin.

I have just got started, and imported by CEL files (affymetrix data); however, when i try to run any of the quality check tools i get the following error and the program closes.

<<
QC process: batchQCscript Thread-7failed!Exit code:1

Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: Biostrings Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from package:base : cbind, duplicated, order, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int, sapply, sort, table, unique Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain sySYNG005a Library - package sysyng005acdf not installed Bioconductor - sysyng005acdf not available Calls: checkOversaturation -> pm -> pm -> .local -> getCdfInfo Execution halted
>>

I am connected to the internet so assumed the CDF files would be downloaded, so am unsure what this error means. If you could direct me as to what to do from here or what i am doing wrong i would be grateful.

Thanks
Dan

Hi Dan,

thanks for your interest in using Robin. The error message indicates that the data your tried to
analyse originates from an Affy chip that is called "sySYNG005a". I checked the bioconductor
web page (http://www.bioconductor.org/packages/2.6/data/annotation/) and found out that this
platform is not (yet) supported by the bioconductor framework. Unfortunately, there is no simple
way to incorporate new platforms since this requires the generation of a new CDF environment for
R. If you supply the CDF file i can create such an environment.

Best greetings,
Marc