[BioC] affy package and porcine arrays

[James W. MacDonald]

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.

Best,

Jim


> 
> 
>>On Mar 30, 2006, at 3:21 PM, David Carter wrote:
>>
>>
>>>Hello,
>>>I am getting some errors using the affy library with porcine arrays:
>>>Error in getCdfInfo(object) : Could not obtain CDF environment,  
>>>problems
>>>encountered:
>>>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
>>>http://www.bioconductor.org/repository/devel/package/Win32 in:
>>>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.
>>
>>Anyway, try
>>  source("http://www.bioconductor.org/biocLite.R")
>>  biocLite("porcinecdf")
>>
>>/Kasper
>>
>>
>>
>>
>>>-- 
>>>David Carter
>>>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
>>>http://www.lrgc.ca
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
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>>>Search the archives: http://news.gmane.org/ 
>>>gmane.science.biology.informatics.conductor
>>
>>
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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