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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.