I also tried put the cdf file in the HG-U133_Plus_2 folder directly as u see in the path but same error * > pathAC <- Arguments$getReadablePath("AromaAnalysis/HG-U133_Plus_2", mustExist=TRUE)*
*[2013-05-01 13:20:42] Exception: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2')* * * * at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, * ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from '<text>' at #01. Arguments$getReadablePath("AromaAnalysis/HG-U133_Plus_2", mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' > getwd() [1] "C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2" On Wednesday, May 1, 2013 1:13:18 PM UTC+1, nawin MOHAMMED wrote: > > > Hi Henrik > > > i changed the directory as you told me but i got this error ?? > > ' > > pathAC <- > Arguments$getReadablePath("AromaAnalysis/ChipType/HG-U133_Plus_2", > mustExist=TRUE) > [2013-05-01 13:11:50] Exception: Pathname not found: > AromaAnalysis/ChipType/HG-U133_Plus_2 (none of the parent directories > [AromaAnalysis/ChipType/] exist; current directory is > 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2') > > at #05. getReadablePathname.Arguments(static, path = path, mustExist = > mustExist, > ...) > - getReadablePathname.Arguments() is in environment 'R.utils' > > at #04. getReadablePathname(static, path = path, mustExist = mustExist, > ...) > - getReadablePathname() is in environment 'R.utils' > > at #03. getReadablePath.Arguments(static, ...) > - getReadablePath.Arguments() is in environment 'R.utils' > > at #02. getReadablePath(static, ...) > - getReadablePath() is in environment 'R.utils' > - originating from '<text>' > > at #01. > Arguments$getReadablePath("AromaAnalysis/ChipType/HG-U133_Plus_2", > mustExist = TRUE) > - Arguments$getReadablePath() is local of the calling function > > Error: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of > the parent directories [AromaAnalysis/ChipType/] exist; current directory > is 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2') > In addition: Warning messages: > 1: In is.na(parent) : > is.na() applied to non-(list or vector) of type 'NULL' > 2: In is.na(parent) : > is.na() applied to non-(list or vector) of type 'NULL' > > getwd() > [1] "C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2" > > > > > I don't know why that happen > > On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote: >> >> Hi. >> >> On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED <naw...@gmail.com> >> wrote: >> > 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 ?? >> >> What you're missing in "Aroma.affymetrix searches for CDF files in the >> annotationData/ directory of the current working directory" is the >> part that says ***of the current working directory***. In other >> words, in your current working directory (i.e. getwd()) you should see >> subdirectory "annotationData" if you call list.files(). You may find >> the following page useful too: >> >> http://aroma-project.org/troubleshooting/DirectoryStructures >> >> >> >> Also, I strongly recommend to put your data files (annotationData/, >> rawData/, etc.) somewhere else than where R installs packages. Right >> now you seem to place them in: >> >> >> C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 >> >> >> >> The directory 'C:/Users/nwayyin/Documents/R/win-library/3.0/' is where >> R install packages and you shouldn't add/remove things from there. >> For instance, if you uninstall aroma.affymetrix then all your data may >> disappear as well. Instead, let your working directory be something >> like: >> >> C:/Users/nwayyin/AromaAnalysis/ >> >> and let that be your working directory in R. >> >> /Henrik >> >> > 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> >> 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 >> >> > 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. >> >> > 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. >> > >> > >> > 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 >> > 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. >> > 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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