[R] Error in affypdnn package

[Henrik Bengtsson]

Hi,

repost your question to the Bioconductor mailing list instead, and
your chances for getting help will be much greater:

  http://bioconductor.org/docs/mailList.html

/Henrik

On Tue, Jul 6, 2010 at 9:06 AM, Hasan, Ahmed Ryadh - hasar001
<Ahmed.Hasan at postgrads.unisa.edu.au> wrote:
> Dear all,
> I am a PhD student working with Affymetrix HGU133atag array for analyzing the Latin square experiment.
>
> I was trying to generate gene expression index for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error-
>
>
>> library(affypdnn)
> Loading required package: affy
> Loading required package: Biobase
> Welcome to Bioconductor
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
> registering new summary method 'pdnn'.
> registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
>> library(hgu133atagprobe)
> Loading required package: AnnotationDbi
>> energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u133a.txt", package = "affypdnn")
>> params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack = "hgu133aprobe")
> Calculating chip type specific parameters, (may take some time)...
> |                    |
> |Error in object$call : $ operator not defined for this S4 class
>>
> After this, I also tried to do it for hgu95av2 array as described in the package manual-
>
>> library(affypdnn)
> Loading required package: affy
> Loading required package: Biobase
> Welcome to Bioconductor
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
> registering new summary method 'pdnn'.
> registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
>> library(hgu95av2probe)
> Loading required package: AnnotationDbi
>> energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u95av2.txt", package = "affypdnn")
>> params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack = "hgu95av2probe")
> Calculating chip type specific parameters, (may take some time)...
> |                    |
> |Error in object$call : $ operator not defined for this S4 class
>>
> Please help me to get rid of this error(Error in object$call : $ operator not defined for this S4 class).
>
> Best regards,
>
> Ahmed Ryadh Hasan
>
> PhD Student,
> Knowledge-Based Intelligent Engineering Systems centre (KES)
> Mawson Lakes Campus, University of South Australia,
> Mawson Lakes, SA 5095
>
> Phone: +61 8 8302 8332 (Office)
>       +61 8 8359 5747 (Home)
>       +61 4 3006 4390 (Cell)
>
>        [[alternative HTML version deleted]]
>
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