[BioC] ReadAffy problem again

[Dick Beyer]

Hi,

I can reproduce this if the simpleaffy package is loaded.  If I just load the affy package, then this problem goes away.

Hope this helps,
Dick

*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
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http://staff.washington.edu/~dbeyer
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On Thu, 9 Nov 2006, Martin Morgan wrote:

> I can't reproduce this reliably on my end, so don't really know what
> is happening; does the problem persist after
>
>> update.packages()
>
> ? As a workaround, does it help to
>
>> library(Biobase)
>
> first?
>
> Martin
>
> "D.Enrique ESCOBAR ESPINOZA" <escobarebio at yahoo.com> writes:
>
>> can someone help me solve this mystery,
>> i was using it very well but something has changed
>> and it is not working any more
>> can someone help me,
>> the trgt file contains the abolute path to each cel.gz file in each
>> line...
>> ******************************
>>> print(myTarget);
>> "../VESICULES.trgt"
>>> print("Reading location for *CEL.gz!")	;
>> "Reading location for *CEL.gz!"
>>> CELlist		<- scan(file=myTarget,what=list("c"),sep="\n",quiet=TRUE)	;
>>> print(CELlist);
>> [1]
>> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX0Z02C1.CEL.gz"
>> [2]
>> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX1Z02C1.CEL.gz"
>> [3]
>> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX2Z02C1.CEL.gz"
>> [4]
>> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX3Z02C1.CEL.gz"
>> [5]
>> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX4Z02C1.CEL.gz"
>> [6]
>> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX5Z02C1.CEL.gz"
>> [7]
>> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX6Z02C1.CEL.gz"
>>> print("Reading location for *CEL.gz!!")	;
>> "Reading location for *CEL.gz!!"
>>> Data		<- ReadAffy(filenames=cels)	;
>> Error in function (classes, fdef, mtable)  :
>>         unable to find an inherited method for function "pData", for
>> signature "phenoData"
>> Execution halted
>>
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>
> --
> Martin T. Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
>