[BioC] affy package and porcine arrays
James W. MacDonald
jmacdon at med.umich.edu
Tue Apr 11 19:43:40 CEST 2006
David Carter wrote:
> Thanks for the suggestions.
> I have updated to R 2.2.1. I have tried biocLite and get the following
> error when running QCReport:
> Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
> chip type: porcinecdf
> Error in plot(qc(object)) : unable to find the argument 'x' in selecting
> a method for function 'plot'
> Any suggestions?
This error indicates that simpleaffy doesn't contain the QC parameters
for this particular chip, so for now you won't be able to do the QC
stuff. You might contact the maintainer (Crispin Miller) directly to see
if they can be added.
>>On Mar 30, 2006, at 3:21 PM, David Carter wrote:
>>>I am getting some errors using the affy library with porcine arrays:
>>>Error in getCdfInfo(object) : Could not obtain CDF environment,
>>>Specified environment specified did not contain Porcine
>>>Library - package porcinecdf not installed
>>>Data for package affy did not contain Porcine
>>>Bioconductor - porcinecdf not available
>>>In addition: Warning message:
>>>Failed to read replisting at
>>>getReplisting(repURL, repFile, method = method)
>>>I am using R version 2.0.1. How do I get the porcine CDF installed?
>>That is really old. You should update, espcially because newer
>>version of affy/Bioconductor will not work with R this old.
>>>London Regional Genomics Centre
>>>Robarts Research Institute, Room 4.01
>>>PO Box 5015, 100 Perth Drive
>>>London, Ontario, Canada, N6A 5K8
>>>phone: (519) 663-3253
>>>fax: (519) 663-3037
>>>dcarter at robarts.ca
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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