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Question: Error in Expression File Creator
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11 months ago by
parin.kamseng0 wrote:

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

written 11 months ago by parin.kamseng0

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