Hi, Please respect the people who are trying to help you out by not sending an email to the list every time you are trying a new (random) command, especially since you are not following the advice which is given to you.
As Henrik suggested, 1. put "your data files (annotationData/, rawData/, etc.)" in "C:/Users/nwayyin/AromaAnalysis/" This means that you should have: "C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2" This is not what you have right now ! and then, still quoting Henrik, 2. "let that be your working directory in R." This means that "getwd()" should say "C:/Users/nwayyin/AromaAnalysis" This is not what you did either ! Please make sure that you did what has been suggested. Thanks, Pierre On Wed, May 1, 2013 at 2:27 PM, nawin MOHAMMED <nawi...@gmail.com> wrote: >> getwd() > [1] "C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2" >> chipType <- "HG-U133_Plus_2" >> chipTypeS <- gsub(",.*", "", chipType) >> path <- Arguments$getReadablePath(chipTypeS, path=pathAC, mustExist=TRUE) > Error in getReadablePath.Arguments(static, ...) : > object 'pathAC' not found > > > > > > > On Wednesday, May 1, 2013 1:22:08 PM UTC+1, nawin MOHAMMED wrote: >> >> I also tried put the cdf file in the HG-U133_Plus_2 folder directly >> as u see in the path but same error >> > pathAC <- Arguments$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. > > > 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. 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