[BioC] affy package and porcine arrays
David Carter
dcarter at robarts.ca
Tue Apr 11 22:37:13 CEST 2006
Thanks Craig,
I believe I altered the 3 files with the correct information, but now am
getting this error:
Error in FUN(X[[4]], ...) : subscript out of bounds
Error in plot(qc(object)) : unable to find the argument 'x' in selecting
a method for function 'plot'
You suggested to use an array with the same number of features, but
don't all the Affy arrays have different numbers of features? Please
correct me if I am wrong. I copied and altered the last line which was
a Rat array. This error looks like I am telling it the wrong number of
features. Any suggestions on where I can correct this?
Sincerely,
David Carter
Craig Parman wrote:
> David,
>
> If look in the ../library/simpleaffy/data directory there are three
> files that contain the qc parameters. You should be able to add a
> line to each to get the package working until it is updated. I would
> copy a line from a different array with the sample number of features
> and modify the cdf name to "porcinecdf" For the spikes and qc.probes
> files just change the probeset names for the controls to match array
> data. That should get it working.
>
> btw - make a backup of the files before you change them.
>
>
> Craig
>
>
>
> ----- Original Message ----- From: "David Carter" <dcarter at robarts.ca>
> To: "Bioconductor list serv" <bioconductor at stat.math.ethz.ch>
> Sent: Tuesday, April 11, 2006 1:05 PM
> Subject: Re: [BioC] affy package and porcine arrays
>
>
>> 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
>>
>> _______________________________________________
>> 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
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