Error in Expression File Creator
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@parinkamseng-14554
Last seen 7.0 years ago


I am using ExpressionFileCreator to creates a RES or GCT file from a set of Affymetrix CEL files. Then I get the following error that I cannot understantand:

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/src/contrib
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain Clariom_S_Human
Library - package clariomshumancdf not installed
Bioconductor - clariomshumancdf not available
Calls: parseCmdLine ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo
Execution halted

I would appreciate any help in figuring out what this means and how to avoid the error.

Thank you

microarray software error affymetrix microarrays • 1.6k views
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Which Bioconductor package are you using? Could you please provide your full code?

Expression File Creator is (also) a module of GenePattern from the Broad Institute, and this apparently is not compatible with the new generation of Affymetrix arrays: http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/ExpressionFileCreator/12

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