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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