Note that there should be/is a comma after the chip type prefix
'RaGene-1_0-st-v1', so rename that 'RaGene-1_0-st-v1.r3.cdf' to
'RaGene-1_0-st-v1,r3.cdf' and retry.

You find some information on this in
http://aroma-project.org/setup/annotationData and illustrated in
http://aroma-project.org/vignettes/GeneSTArrayAnalysis

Hope this helps

Henrik


On Sun, Sep 14, 2014 at 10:11 PM, jjspring OH <sshshoh1...@gmail.com> wrote:
> Hi
>
> I am working on aroma.affymetrix package,
> btw, it seems like i set up the annotationDat and rawData directory under
> the current working directory(/arom-anal) right,
> but not working when i upload cdf file with cdf <-
> AffymetrixCdfFile$byChipType(chipType, tags="r3")
>
> Please see my sessionInfo() in R and also, directory information as below:
>
> Plus, in order to easily describe the case, i have attached working
> directory image files in which annotation and cel files exist as well,
>
> Please let me know if there is something wrong,
>
>
> = >>>
>
>
>
>
> In R,
>
>
>
>> verbose <- Arguments$getVerbose(-8, timestamp=T)
>
>> chipType <- "RaGene-1_0-st-v1"
>
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
>
> [2014-09-15 14:03:25] Exception: Failed to create AffymetrixCdfFile object.
> Could not locate an annotation data file for chip type 'RaGene-1_0-st-v1'
> with tags 'r3' and with filename extension 'cdf'.
>
>
>   at #03. byChipType.UnitAnnotationDataFile(static, ...)
>
>           - byChipType.UnitAnnotationDataFile() is in environment
> 'aroma.core'
>
>
>   at #02. byChipType(static, ...)
>
>           - byChipType() is in environment 'aroma.core'
>
>           - originating from '<text>'
>
>
>   at #01. AffymetrixCdfFile$byChipType(chipType, tags = "r3")
>
>           - AffymetrixCdfFile$byChipType() is local of the calling function
>
>
> Error: Failed to create AffymetrixCdfFile object. Could not locate an
> annotation data file for chip type 'RaGene-1_0-st-v1' with tags 'r3' and
> with filename extension 'cdf'.
>
>>
>
>
>
>
>
>
>
>
>> help(AffymetrixCdfFile)
>
>> getwd()
>
> [1] "/arom-anal"
>
>> quit()
>
> Save workspace image? [y/n/c]: n
>
> verdas-MacBook-Pro:arom-anal sungheeoh$ ls
>
> annotationData rawData
>
> verdas-MacBook-Pro:arom-anal sungheeoh$ cd annotationData/
>
> verdas-MacBook-Pro:annotationData sungheeoh$ cd ..
>
> verdas-MacBook-Pro:arom-anal sungheeoh$ cd rawData/
>
> verdas-MacBook-Pro:rawData sungheeoh$ ls
>
> tissues
>
> verdas-MacBook-Pro:rawData sungheeoh$ cd tissues
>
> verdas-MacBook-Pro:tissues sungheeoh$ ls
>
> RaGene-1_0-st-v1
>
> verdas-MacBook-Pro:tissues sungheeoh$ cd RaGene-1_0-st-v1/
>
> verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ ls
>
> CS _ 10_(RaGene-1_0-st-v1).CEL CS _ 7_(RaGene-1_0-st-v1).CEL NS _
> 1_(RaGene-1_0-st-v1).CEL NS _ 4_(RaGene-1_0-st-v1).CEL
>
> CS _ 12_(RaGene-1_0-st-v1).CEL CS _ 8_(RaGene-1_0-st-v1).CEL NS _
> 3_(RaGene-1_0-st-v1).CEL NS _ 5_(RaGene-1_0-st-v1).CEL
>
> verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ cd ..
>
> verdas-MacBook-Pro:tissues sungheeoh$ cd ..
>
> verdas-MacBook-Pro:rawData sungheeoh$ cd ..
>
> verdas-MacBook-Pro:arom-anal sungheeoh$ cd annotationData/
>
> verdas-MacBook-Pro:annotationData sungheeoh$ ls
>
> chipTypes
>
> verdas-MacBook-Pro:annotationData sungheeoh$ cd chipTypes/
>
> verdas-MacBook-Pro:chipTypes sungheeoh$ ls
>
> RaGene-1_0-st-v1
>
> verdas-MacBook-Pro:chipTypes sungheeoh$ cd RaGene-1_0-st-v1/
>
> verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ ls
>
> RaGene-1_0-st-v1.r3.cdf
>
> verdas-MacBook-Pro:RaGene-1_0-st-v1 sungheeoh$ R
>
>
>
>
> R version 3.1.1 (2014-07-10)
>
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
> Thanks, Sunghee
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
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-- 
-- 
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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