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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