hi Pierre, the anootationData is allocated by default in the aroma.affymetrix ?? is it ??? as its declare in the page of aroma :
Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory. Place the CDF for chip type <chipType> in a directory of format: annotationData/chipTypes/<chip type>/ and my location is "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 i just creat new folder in annotation data with name chip type and inside it another folder with chip name ??? iam just confused ?? why this error occur please if you know the cause of problem please tell me On Tuesday, April 30, 2013 3:16:00 PM UTC+1, Pierre Neuvial wrote: > > Hi, > > Quoting myself, > > "1. Read carefully the setup page: http://www.aroma-project.org/setup, > and follow the links in that page." > > The first link "Location of annotation data files" explains where > annotation data files should be located. > > Best, > > Pierre > > > On Tue, Apr 30, 2013 at 2:10 PM, nawin MOHAMMED > <naw...@gmail.com<javascript:>> > wrote: > > > > i also down load the CDF from affymetrix but its not working same > > problem > > > > Error: Failed to create AffymetrixCdfFile object. Could not locate an > > annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and > > with filename extension 'cdf'. > >> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2",tags="full") > > [2013-04-30 13:08:07] Exception: Failed to create AffymetrixCdfFile > object. > > Could not locate an annotation data file for chip type 'HG-U133_Plus_2' > with > > tags 'full' and with filename extension 'cdf'. > > > > at #03. byChipType.UnitAnnotationDataFile(static, ...) > > - byChipType.UnitAnnotationDataFile() is in environment > > 'aroma.core' > > > > at #02. byChipType(static, ...) > > - byChipType() is in environment 'aroma.core' > > - originating from '<text>' > > > > at #01. AffymetrixCdfFile$byChipType("HG-U133_Plus_2", tags = "full") > > - AffymetrixCdfFile$byChipType() is local of the calling > function > > > > Error: Failed to create AffymetrixCdfFile object. Could not locate an > > annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and > > with filename extension 'cdf'. > >> getwd() > > [1] > > > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/CD_hgu133a2_libraryfile" > > > >> > > > > > > On Tuesday, April 30, 2013 8:40:35 AM UTC+1, Pierre Neuvial wrote: > >> > >> Hi, > >> > >> Please create a new thread (with a relevant subject line) instead of > >> replying to an unrelated one. > >> > >> See below. > >> > >> On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED <naw...@gmail.com> > wrote: > >> > > >> > > >> > Greeting , > >> > > >> > iam a Phd student , i try implement aroma package but its not > working > >> > with > >> > me , i don't know where is the error, and i have question the > >> > shiptype > >> > folder is not exist be default in annotationdata, i just create > a > >> > folder in annotation data name it chiptype and i put the cdf file in > it > >> > , is > >> > that possible ??? please i need your advice this is my program > >> > > >> > > >> > > >> > >> Yes, that's what you should do. Here is some general advice that > >> could save you lots of time: > >> > >> 1. Read carefully the setup page: http://www.aroma-project.org/setup, > >> and follow the links in that page. > >> > >> 2. Be really careful with the folder and file names: "annotationData" > >> is not the same as "annotationdata", etc. The same holds for function > >> names in the code you have pasted below, for example > >> "AffymetrixcdfFile" is not the same as "AffymetrixCdfFile", etc... > >> > >> 3. Do not try to guess/invent code lines if you are not familiar with > >> the aroma framework. Instead, try to reproduce a vignette, for > >> example this one: > >> http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis > >> > >> Best, > >> > >> Pierre > >> > >> >> getwd() > >> > [1] > >> > > >> > > "C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType" > > > >> >> ChipType(""HG-U133_Plus_2") > >> > Error: unexpected symbol in "ChipType(""HG" > >> >> ChipType("HG-U133_Plus_2") > >> > Error: could not find function "ChipType" > >> >> chipType("HG-U133_Plus_2") > >> > Error: could not find function "chipType" > >> >> library(aroma.affymetrix) > >> >> ChipeType("HG-U133_Plus_2") > >> > Error: could not find function "ChipeType" > >> >> chipType<-"HG-U133_Plus_2" > >> >> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2") > >> > Error: object 'AffymetrixcdfFile' not found > >> >> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2") > >> > Error: object 'AffymetrixcdfFile' not found > >> >> cdf<-AffymetrixcdfFile$byChipType("HG-U133_Plus_2") > >> > Error: object 'AffymetrixcdfFile' not found > >> >> cdf<-HG-U133_Plus_2$bychipType("HG-U133_Plus_2") > >> > Error: object 'HG' not found > >> >> cdf<-AffymetrixcdfFile$bychipType("HG-U133_Plus_2", tags=ChipType) > >> > Error: object 'AffymetrixcdfFile' not found > >> >> > >> > > >> > the error is with cdf file which can not be read > >> > i download all the package > >> > > >> > source("http://bioconductor.org/biocLite.R";) > >> > > >> > biocLite("biomaRt") > >> > > >> > hbInstall("aroma.affymetrix") > >> > > >> > thank you > >> > > > > > -- > > -- > > 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-af...@googlegroups.com<javascript:> > > 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-affymetr...@googlegroups.com <javascript:>. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > -- -- 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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