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)
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