Hi. On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED <nawi...@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-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/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-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/groups/opt_out.
