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
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