[BioC] affy package and porcine arrays

[David Carter]

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?

>
> 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
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
>
>

-- 
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


>
> 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
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
>
>

-- 
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


>
> 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
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
>
>

-- 
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